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  2020 (11)
Understanding ML Driven HPC: Applications and Infrastructure. Jha, S.; and Fox, G. In pages 421-427, 3 2020. Institute of Electrical and Electronics Engineers (IEEE)
Understanding ML Driven HPC: Applications and Infrastructure [pdf]Paper   Understanding ML Driven HPC: Applications and Infrastructure [link]Website   doi   link   bibtex   abstract   2 downloads  
Learning Everywhere: A Taxonomy for the Integration of Machine Learning and Simulations. Fox, G.; and Jha, S. In pages 439-448, 3 2020. Institute of Electrical and Electronics Engineers (IEEE)
Learning Everywhere: A Taxonomy for the Integration of Machine Learning and Simulations [pdf]Paper   Learning Everywhere: A Taxonomy for the Integration of Machine Learning and Simulations [link]Website   doi   link   bibtex   abstract   2 downloads  
Object Classifications by Image Super-Resolution Preprocessing for Convolutional Neural Networks. Na, B.; and Fox, G., C. Advances in Science, Technology and Engineering Systems Journal, 5(2): 476-483. 2020.
doi   link   bibtex   2 downloads  
Targeted High-Resolution Structure from Motion Observations over the M w 6.4 and 7.1 Ruptures of the Ridgecrest Earthquake Sequence. Donnellan, A.; Lyzenga, G.; Ansar, A.; Goulet, C.; Wang, J.; and Pierce, M. Seismological Research Letters,1-9. 2020.
Targeted High-Resolution Structure from Motion Observations over the M w 6.4 and 7.1 Ruptures of the Ridgecrest Earthquake Sequence [pdf]Paper   Targeted High-Resolution Structure from Motion Observations over the M w 6.4 and 7.1 Ruptures of the Ridgecrest Earthquake Sequence [pdf]Website   doi   link   bibtex   abstract  
Ground Deformation Data from GEER Investigations of Ridgecrest Earthquake Sequence. Brandenberg, S., J.; Stewart, J., P.; Wang, P.; Nweke, C., C.; Hudson, K.; Goulet, C., A.; Meng, X.; Davis, C., A.; Ahdi, S., K.; Hudson, M., B.; Donnellan, A.; Lyzenga, G.; Pierce, M.; Wang, J.; Winters, M., A.; Delisle, M.; Lucey, J.; Kim, Y.; Gallien, T., W.; Lyda, A.; Yeung, J., S.; Issa, O.; Buckreis, T.; and Yi, Z. Seismological Research Letters. 2 2020.
doi   link   bibtex   abstract  
Self‐regulated studying behavior, and the social norms that influence it. Eyink, J., R.; Motz, B., A.; Heltzel, G.; and Liddell, T., M. Journal of Applied Social Psychology, 50(1): 10-21. 1 2020.
Self‐regulated studying behavior, and the social norms that influence it [link]Website   doi   link   bibtex   abstract  
What college students say, and what they do: Aligning self-regulated learning theory with behavioral logs. Quick, J.; Motz, B.; Israel, J.; and Kaetzel, J. In International Conference on Learning Analytics & Knowledge, pages 534-543, 3 2020. Association for Computing Machinery
What college students say, and what they do: Aligning self-regulated learning theory with behavioral logs [pdf]Paper   What college students say, and what they do: Aligning self-regulated learning theory with behavioral logs [link]Website   doi   link   bibtex   abstract  
Scalable Quality Assurance for Neuroimaging (SQAN): automated quality control for medical imaging. Gopu, A.; Young, M., D.; Avena-Koenigsberger, A.; Perigo, R., W.; West, J., D.; Paramasivam, M.; Hayashi, S.; and Henschel, R. In Deserno, T., M.; and Chen, P., editor(s), Medical Imaging 2020: Imaging Informatics for Healthcare, Research, and Applications, volume 11318, pages 6, 3 2020. SPIE
Scalable Quality Assurance for Neuroimaging (SQAN): automated quality control for medical imaging [pdf]Paper   Scalable Quality Assurance for Neuroimaging (SQAN): automated quality control for medical imaging [link]Website   doi   link   bibtex   abstract   1 download  
Technical Report: XSEDE Return on Investment (Proxy) Data and Analysis Methods, July 2014 to August 2019. Wernert, J., A.; Costa, Claudia M.; McMullen, Donald F.; Stewart, C., A.; Blood, P., D.; and Sinkovits, Robert; Mehringer, Susan H.; Knepper, R. Technical Report 2020.
Technical Report: XSEDE Return on Investment (Proxy) Data and Analysis Methods, July 2014 to August 2019 [link]Website   link   bibtex  
2020 External Review of the Pervasive Technology Institute. Stewart, C., A.; Slavin, S.; and Ping, R. Technical Report 5 2020.
2020 External Review of the Pervasive Technology Institute [pdf]Paper   2020 External Review of the Pervasive Technology Institute [link]Website   link   bibtex   abstract  
Indiana University Pervasive Technology Institute preproposal and proposal management, documentation, and templates. Stewart, C., A.; Miller, T.; Snapp-Childs, W.; Jankowski, H.; and Husk, M. Technical Report 2020.
Indiana University Pervasive Technology Institute preproposal and proposal management, documentation, and templates [link]Website   link   bibtex   abstract   3 downloads  
  2019 (64)
Experiences from scaling scale Science Gateway operations. Marru, S.; Piece, M.; Abeysinghe, E.; Pamidighantam, S.; Christie, M.; and Wannipurage, D. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. ACM Press
Experiences from scaling scale Science Gateway operations [pdf]Paper   Experiences from scaling scale Science Gateway operations [link]Website   doi   link   bibtex   abstract  
Towards a science gateway reference architecture. Pierce, M., E.; Miller, M., A.; Brookes, E., H.; Wong, M.; Afgan, E.; Liu, Y.; Gesing, S.; Dahan, M.; Walker, T.; and Marru, S. In CEUR Workshop Proceedings, volume 2357, 2019. CEUR-WS
link   bibtex   abstract  
Programmable Education Infrastructure: Cloud resources as HPC Education Environments. Coulter, E.; Knepper, R.; and Fischer, J. The Journal of Computational Science Education, 10(1): 107-107. 1 2019.
Programmable Education Infrastructure: Cloud resources as HPC Education Environments [pdf]Paper   Programmable Education Infrastructure: Cloud resources as HPC Education Environments [link]Website   doi   link   bibtex   abstract  
How the Science Gateways Community Institute Supports Those Who Are Creating Websites to Access Shared Resources. Lawrence, K., A.; Mullinix, N.; Dahan, M.; Hayden, L.; Pierce, M.; Wilkins-Diehr, N.; and Zentner, M. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. ACM Press
How the Science Gateways Community Institute Supports Those Who Are Creating Websites to Access Shared Resources [pdf]Paper   How the Science Gateways Community Institute Supports Those Who Are Creating Websites to Access Shared Resources [link]Website   doi   link   bibtex   abstract  
The Distant Reader. Morgan, E., L.; Abeysinghe, E.; Pamidighantam, S.; Coulter, E.; Marru, S.; and Pierce, M. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. ACM Press
The Distant Reader [pdf]Paper   The Distant Reader [link]Website   doi   link   bibtex   abstract  
Research Computing at a Business University. Wells, J.; and Coulter, J., E. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-5, 2019. Association for Computing Machinery (ACM)
Research Computing at a Business University [pdf]Paper   doi   link   bibtex   abstract  
LSU Computational System Biology Gateway for Education. Abeysinghe, E.; Brylinski, M.; Christie, M.; Marru, S.; and Pierce, M. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. ACM Press
LSU Computational System Biology Gateway for Education [pdf]Paper   LSU Computational System Biology Gateway for Education [link]Website   doi   link   bibtex   abstract  
Beyond Campus Bridging: A retrospective of Cyberinfrastructure Integration Efforts. Coulter, J., E.; Knepper, R.; Reynolds, R.; Sprouse, J.; and Bird, S. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. Association for Computing Machinery (ACM)
Beyond Campus Bridging: A retrospective of Cyberinfrastructure Integration Efforts [pdf]Paper   doi   link   bibtex  
A Lightweight Framework for Research Data Management. Nikolov, D.; and Tuna, E. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC '19), pages 1-4, 2019. Association for Computing Machinery (ACM)
A Lightweight Framework for Research Data Management [pdf]Paper   doi   link   bibtex   abstract  
E-RPID PEARC 2019 - The Digital Object Architecture and Enhanced Robust Persistent Identification of Data. Quick, R.; Lannom, L.; Krenz, M.; and Luo, Y. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. ACM Press
E-RPID PEARC 2019 - The Digital Object Architecture and Enhanced Robust Persistent Identification of Data [pdf]Paper   E-RPID PEARC 2019 - The Digital Object Architecture and Enhanced Robust Persistent Identification of Data [link]Website   doi   link   bibtex   abstract  
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. Johri, P.; Marinov, G., K.; Doak, T., G.; and Lynch, M. Genome Biology and Evolution, 11(5): 1398-1416. 2019.
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. [pdf]Paper   Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. [link]Website   doi   link   bibtex   abstract  
Jetstream: A Novel Cloud System for Science. Stewart, C., A.; Hancock, D., Y.; Miller, T.; Fischer, J.; Liming, R., L.; Turner, G.; Lowe, J., M.; Gregory, S.; Skidmore, E.; Vaughn, M.; Stanzione, D.; Merchant, N.; Foster, I.; Taylor, J.; Rad, P.; Brendel, V.; Afgan, E.; Packard, M.; Miller, T.; and Snapp-Childs, W. Contemporary High Performance Computing, pages 189-222. CRC Press, 5 2019.
Contemporary High Performance Computing [link]Website   doi   link   bibtex   abstract   1 download  
Training children aged 5–10 years in manual compliance control to improve drawing and handwriting. Bingham, G., P.; and Snapp-Childs, W. Human Movement Science, 65: 42-50. 6 2019.
Training children aged 5–10 years in manual compliance control to improve drawing and handwriting [pdf]Paper   Training children aged 5–10 years in manual compliance control to improve drawing and handwriting [link]Website   doi   link   bibtex   abstract  
Research Computing Desktops: Demystifying research computing for non-Linux users. Thota, A.; Dietz, D., T.; Phillips, C.; Zhu, X.; Weakley, L., M.; Fulton, B.; Dennis, H., E., C., B.; Huber, L.; Michael, S.; Snapp-Childs, W.; Harrell, S., L.; and Younts, A. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC '19), pages 1-8, 2019. Association for Computing Machinery (ACM)
Research Computing Desktops: Demystifying research computing for non-Linux users [pdf]Paper   doi   link   bibtex   abstract  
A High-Frequency Mobile Phone Data Collection Approach for Research in Social-Environmental Systems: Applications in Climate Variability and Food Security in Sub-Saharan Africa. Giroux, S., A.; Kouper, I.; Estes, L., D.; Schumacher, J.; Waldman, K.; Greenshields, J., T.; Dickinson, S., L.; Caylor, K., K.; and Evans, T., P. Environmental Modelling & Software. 5 2019.
A High-Frequency Mobile Phone Data Collection Approach for Research in Social-Environmental Systems: Applications in Climate Variability and Food Security in Sub-Saharan Africa [link]Website   doi   link   bibtex   abstract  
Safe Open Science for Restricted Data. Plale, B., A.; Dickson, E.; Kouper, I.; Liyanage, S.; Ma, Y.; McDonald, R., H.; Walsh, J., A.; and Withana, S. Data and Information Management, 3(1): 50-60. 2019.
Safe Open Science for Restricted Data [link]Website   doi   link   bibtex  
Twister2: Design of a big data toolkit. Kamburugamuve, S.; Govindarajan, K.; Wickramasinghe, P.; Abeykoon, V.; and Fox, G. Concurrency Computation: Practice and Experience. 2019.
Twister2: Design of a big data toolkit [pdf]Paper   doi   link   bibtex   abstract  
Regge phenomenology of the N∗ and Δ∗ poles. Silva-Castro, J., A.; Fernández-Ramírez, C.; Albaladejo, M.; Danilkin, I., V.; Jackura, A.; Mathieu, V.; Nys, J.; Pilloni, A.; Szczepaniak, A., P.; and Fox, G. Physical Review D, 99(3). 2 2019.
Regge phenomenology of the N∗ and Δ∗ poles [pdf]Paper   doi   link   bibtex   abstract   1 download  
Big Data Benchmarks of High-Performance Storage Systems on Commercial Bare Metal Clouds. Lee, H.; and Fox, G. In IEEE International Conference on Cloud Computing (IEEE CLOUD 2019), 5 2019.
Big Data Benchmarks of High-Performance Storage Systems on Commercial Bare Metal Clouds [pdf]Website   doi   link   bibtex   abstract  
Learning Everywhere Resource for BDEC. Fox, G.; and July, U. Technical Report 2019.
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Harnessing the Computing Continuum for Programming Our World. Beckman, P.; Dongarra, J.; Ferrier, N.; Fox, G.; Moore, T.; Reed, D.; and Beck, M. Technical Report 2019.
Harnessing the Computing Continuum for Programming Our World [pdf]Paper   Harnessing the Computing Continuum for Programming Our World [link]Website   link   bibtex   abstract  
Perspectives on High-Performance Computing in a Big Data World. Fox, G., C. In Proceedings of the 28th International Symposium on High-Performance Parallel and Distributed Computing (HPDC '19), pages 145-145, 2019. Association for Computing Machinery (ACM)
Perspectives on High-Performance Computing in a Big Data World [pdf]Paper   doi   link   bibtex   abstract  
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation: Application Background. Fox, G.; Glazier, J., A.; Kadupitiya, J.; Jadhao, V.; Kim, M.; Qiu, J.; Sluka, J., P.; Somogy, E.; Marathe, M.; Adiga, A.; Chen, J.; Beckstein, O.; Jha, S.; Somogyi, E.; Marathe, M.; Adiga, A.; Chen, J.; Beckstein, O.; and Jha, S. In 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pages 33, 5 2019. IEEE
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation: Application Background [pdf]Paper   Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation: Application Background [link]Website   doi   link   bibtex   abstract  
Machine Learning for Performance Enhancement of Molecular Dynamics Simulations. Kadupitiya, J.; Fox, G., C.; and Jadhao, V. In volume 11537 LNCS, pages 116-130, 2019. Springer Verlag
Machine Learning for Performance Enhancement of Molecular Dynamics Simulations [pdf]Paper   doi   link   bibtex   abstract  
Object Classification by a Super-resolution Method and a Convolutional Neural Networks. Na, B.; and Fox, G., C. International Journal of Data Mining Science, 1(1): 16-23. 2019.
Object Classification by a Super-resolution Method and a Convolutional Neural Networks [pdf]Paper   Object Classification by a Super-resolution Method and a Convolutional Neural Networks [link]Website   link   bibtex   abstract  
Advances in big data programming, system software and HPC convergence. Hsu, C., H.; Fox, G.; Min, G.; and Sharma, S. Journal of Supercomputing, 75(2): 489-493. 2 2019.
Advances in big data programming, system software and HPC convergence [pdf]Paper   doi   link   bibtex   abstract  
Twister2: TSet high-performance iterative dataflow. Wickramasinghe, P.; Kamburugamuve, S.; Govindarajan, K.; Abeykoon, V.; Widanage, C.; Perera, N.; Uyar, A.; Gunduz, G.; Akkas, S.; and Fox, G. In 2019 International Conference on High Performance Big Data and Intelligent Systems, HPBD and IS 2019, pages 55-60, 5 2019. Institute of Electrical and Electronics Engineers Inc.
Twister2: TSet high-performance iterative dataflow [pdf]Paper   doi   link   bibtex   abstract  
Parallel Performance of Molecular Dynamics Trajectory Analysis. Khoshlessan, M.; Paraskevakos, I.; Fox, G., C.; Jha, S.; and Beckstein, O. Technical Report 2019.
Parallel Performance of Molecular Dynamics Trajectory Analysis [pdf]Paper   link   bibtex   abstract  
Trusted CI Experiences in Cybersecurity and Service to Open Science. Adams, A.; Jackson, C.; Kiser, R.; Krenz, M.; Marsteller, J.; Miller, B., P.; Peisert, S.; Russell, S.; Sons, S.; Welch, V.; Zage, J.; Avila, K.; Basney, J.; Brunson, D.; Cowles, R.; Dopheide, J.; Fleury, T.; Heymann, E.; and Hudson, F. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC '19), pages 1-8, 2019. Association for Computing Machinery (ACM)
Trusted CI Experiences in Cybersecurity and Service to Open Science [pdf]Paper   doi   link   bibtex   abstract  
Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences. Rynge, M.; Poehlman, W., L.; Feltus, F., A.; Vahi, K.; Deelman, E.; Mandal, A.; Baldin, I.; Bhide, O.; Heiland, R.; Welch, V.; and Hill, R. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC '19), pages 1-8, 2019. Association for Computing Machinery (ACM)
Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences [pdf]Paper   doi   link   bibtex   abstract  
Intelligent systems for geosciences: An essential research agenda. Gil, Y.; Pierce, S., A.; Babaie, H.; Banerjee, A.; Borne, K.; Bust, G.; Cheatham, M.; Ebert-Uphoff, I.; Gomes, C.; Hill, M.; Horel, J.; Hsu, L.; Kinter, J.; Knoblock, C.; Krum, D.; Kumar, V.; Lermusiaux, P.; Liu, Y.; North, C.; Pankratius, V.; Peters, S.; Plale, B.; Pope, A.; Ravela, S.; Restrepo, J.; Ridley, A.; Samet, H.; and Shekhar, S. Communications of the ACM, 62(1): 76-84. 1 2019.
Intelligent systems for geosciences: An essential research agenda [pdf]Paper   doi   link   bibtex   abstract   19 downloads  
Campus Champions: Building and sustaining a thriving community of practice around research computing and data. Brazil, M.; Smith, J.; Wernert, J.; Brunson, D.; Culich, A.; DeStefano, L.; Jennewein, D.; Jolley, T.; Middelkoop, T.; Neeman, H.; and Rivera, L. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-7, 2019. Association for Computing Machinery (ACM)
Campus Champions: Building and sustaining a thriving community of practice around research computing and data [pdf]Paper   doi   link   bibtex   abstract  
Initial Thoughts on Cybersecurity And Reproducibility. Deelman, E.; Stodden, V.; Taufer, M.; and Welch, V. In Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems (P-RECS '19), pages 13-15, 2019. Association for Computing Machinery (ACM)
Initial Thoughts on Cybersecurity And Reproducibility [pdf]Paper   doi   link   bibtex   abstract  
Data Integrity Threat Model. Welch, V.; and Abhinit, I. Technical Report ScholarWorks, 6 2019.
Data Integrity Threat Model [pdf]Paper   Data Integrity Threat Model [link]Website   link   bibtex   abstract   2 downloads  
A Guide for Software Assurance for SWIP. Heiland, R.; Rynge, M.; Vahi, K.; Deelman, E.; and Welch, V. Technical Report 2019.
A Guide for Software Assurance for SWIP [pdf]Paper   A Guide for Software Assurance for SWIP [link]Website   link   bibtex   abstract  
Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows. Chapp, D.; Rorabaugh, D.; Brown, D., A.; Deelman, E.; Vahi, K.; Welch, V.; and Taufer, M. In Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems - P-RECS '19, pages 1-6, 2019. ACM Press
Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows [pdf]Paper   Applicability Study of the PRIMAD Model to LIGO Gravitational Wave Search Workflows [link]Website   doi   link   bibtex   abstract   2 downloads  
The USD Science Gateway. Kleinsasser, A., A.; Pamidighantam, S.; Jennewein, D., M.; Madison, J., D.; Christie, M.; Abeysinghe, E.; Marru, S.; and Pierce, M. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. ACM Press
The USD Science Gateway [pdf]Paper   The USD Science Gateway [link]Website   doi   link   bibtex   abstract  
Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained. Katz, D., S.; McInnes, L., C.; Bernholdt, D., E.; Mayes, A., C.; Hong, N., P., C.; Duckles, J.; Gesing, S.; Heroux, M., A.; Hettrick, S.; Jimenez, R., C.; Pierce, M.; Weaver, B.; and Wilkins-Diehr, N. Computing in Science & Engineering, 21(2): 8-24. 3 2019.
Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained [pdf]Paper   Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained [link]Website   doi   link   bibtex   abstract  
Towards Run Time Estimation of the Gaussian Chemistry Code for SEAGrid Science Gateway. Beltre, A.; Zaman, S.; Chiu, K.; Pamidighantam, S.; Qiao, X.; and Govindaraju, M. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-8, 2019. ACM Press
Towards Run Time Estimation of the Gaussian Chemistry Code for SEAGrid Science Gateway [pdf]Paper   Towards Run Time Estimation of the Gaussian Chemistry Code for SEAGrid Science Gateway [link]Website   doi   link   bibtex   abstract  
Virtual Clusters in the Jetstream Cloud. Coulter, J., E.; Abeysinghe, E.; Pamidighantam, S.; and Pierce, M. In Proceedings of the Humans in the Loop: Enabling and Facilitating Research on Cloud Computing - HARC '19, pages 1-6, 2019. ACM Press
Virtual Clusters in the Jetstream Cloud [pdf]Paper   Virtual Clusters in the Jetstream Cloud [link]Website   doi   link   bibtex   abstract  
Assessment of financial returns on investments in cyberinfrastructure facilities. Stewart, C., A.; Apon, A.; Payne, R.; Slavin, S., D.; Hancock, D., Y.; Wernert, J.; Furlani, T.; Lifka, D.; Sill, A.; Berente, N.; McMullen, D., F.; and Cheatham, T. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-8, 2019. ACM Press
Assessment of financial returns on investments in cyberinfrastructure facilities [pdf]Paper   Assessment of financial returns on investments in cyberinfrastructure facilities [link]Website   doi   link   bibtex   abstract  
The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Avesani, P.; McPherson, B.; Hayashi, S.; Caiafa, C., F.; Henschel, R.; Garyfallidis, E.; Kitchell, L.; Bullock, D.; Patterson, A.; Olivetti, E.; Sporns, O.; Saykin, A., J.; Wang, L.; Dinov, I.; Hancock, D.; Caron, B.; Qian, Y.; and Pestilli, F. Scientific Data, 6(1): 69. 12 2019.
The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services [pdf]Paper   The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services [link]Website   doi   link   bibtex   abstract   1 download  
Assessment of non-financial returns on cyberinfrastructure. Stewart, C., A.; Apon, A.; Hancock, D., Y.; Furlani, T.; Sill, A.; Wernert, J.; Lifka, D.; Berente, N.; Cheatham, T.; and Slavin, S., D. In Proceedings of the Humans in the Loop: Enabling and Facilitating Research on Cloud Computing - HARC '19, pages 1-10, 2019. ACM Press
Assessment of non-financial returns on cyberinfrastructure [pdf]Paper   Assessment of non-financial returns on cyberinfrastructure [link]Website   doi   link   bibtex   abstract  
Implementing a Flexible, Fault Tolerant Job Management System for Science Gateways. Wannipurage, D.; Marru, S.; Piece, M.; Abeysinghe, E.; Pamidighantam, S.; Christie, M.; Shenoy, G.; Dhamnaskar, A.; and Jayathilaka, L. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-8, 2019. ACM Press
Implementing a Flexible, Fault Tolerant Job Management System for Science Gateways [pdf]Paper   Implementing a Flexible, Fault Tolerant Job Management System for Science Gateways [link]Website   doi   link   bibtex   abstract  
InterACTWEL Science Gateway for Adaptation Planning in Food-Energy-Water Sectors of Local Communities. Babbar-Sebens, M.; Rivera, S.; Abeysinghe, E.; Marru, S.; Pierce, M.; Coulter, E.; Farahani, M.; Wannipurage, D.; and Christie, M. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) - PEARC '19, pages 1-4, 2019. Association for Computing Machinery (ACM)
InterACTWEL Science Gateway for Adaptation Planning in Food-Energy-Water Sectors of Local Communities [pdf]Paper   doi   link   bibtex   abstract  
Science gateways: Sustainability via on-campus teams. Gesing, S.; Lawrence, K.; Dahan, M.; Pierce, M., E.; Wilkins-Diehr, N.; and Zentner, M. Future Generation Computer Systems, 94: 97-102. 5 2019.
Science gateways: Sustainability via on-campus teams [pdf]Paper   Science gateways: Sustainability via on-campus teams [link]Website   doi   link   bibtex   abstract  
Managing authentication and authorization in distributed science gateway middleware. Christie, M., A.; Bhandar, A.; Nakandala, S.; Marru, S.; Abeysinghe, E.; Pamidighantam, S.; and Pierce, M., E. Future Generation Computer Systems. 10 2019.
Managing authentication and authorization in distributed science gateway middleware [pdf]Paper   Managing authentication and authorization in distributed science gateway middleware [link]Website   doi   link   bibtex   abstract  
Scientific image restoration anywhere. Abeykoon, V.; Liu, Z.; Kettimuthu, R.; Fox, G.; and Foster, I. In Proceedings of XLOOP 2019: 1st Annual Workshop on Large-Scale Experiment-in-the-Loop Computing, Held in conjunction with SC 2019: The International Conference for High Performance Computing, Networking, Storage and Analysis, pages 8-13, 11 2019. Institute of Electrical and Electronics Engineers Inc.
Scientific image restoration anywhere [pdf]Paper   Scientific image restoration anywhere [link]Website   doi   link   bibtex   abstract  
Benchmarking Deep Learning for Time Series: Challenges and Directions. Huang, X.; Fox, G., C.; Serebryakov, S.; Mohan, A.; Morkisz, P.; and Dutta, D. In Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019, pages 5679-5682, 12 2019. Institute of Electrical and Electronics Engineers Inc.
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Streaming Machine Learning Algorithms with Big Data Systems. Abeykoon, V.; Laszewski, G., V.; Kamburugamuve, S.; Govindrarajan, K.; Wickramasinghe, P.; Widanage, C.; Perera, N.; Uyar, A.; Gunduz, G.; and Akkas, S. In Proceedings - 2019 IEEE International Conference on Big Data, Big Data 2019, pages 5661-5666, 12 2019. Institute of Electrical and Electronics Engineers Inc.
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Automated Ice-Bottom Tracking of 2D and 3D Ice Radar Imagery Using Viterbi and TRW-S. Berger, V.; Xu, M.; Al-Ibadi, M.; Chu, S.; Crandall, D.; Paden, J.; and Fox, G., C. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 12(9): 3272-3285. 9 2019.
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InterACTWEL Science Gateway for Adaptation Planning in Food-Energy-Water Sectors of Local Communities: Data, Methods, Lessons Learned and Future Directions. Rivera, S., J.; Giles, N., A.; Tilt, J.; Reimer, J.; Murthy, G.; Mukhopadhyay, S.; Durresi, A.; Marru, S.; Pierce, M., E.; and Babbar-Sebens, M. In American Geophysical Union Fall Meeting, 12 2019. American Geophysical Union
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CyberWater—An open and sustainable framework for diverse data and model integration. Luna, D.; Chen, R.; Yuan, C.; Liang, Y.; Liang, X.; Bales, J.; Castronova, A., M.; Demir, I.; Hooper, R., P.; Krajewski, W., F.; Lin, L.; Mantilla, R.; Pamidighantam, S.; Song, F.; and Zhang, Y. In American Geophysical Union Fall Meeting, 12 2019. AGU
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Stakeholder-Driven Adaptation Planning of Food-Energy-Water Nexus in Local Communities. Babbar-Sebens, M.; Rivera, S., J.; Giles, N., A.; Tilt, J.; Reimer, J.; Murthy, G.; Mukhopadhyay, S.; Durresi, A.; Marru, S.; and Pierce, M., E. In American Geophysical Union Fall Meeting, 12 2019. AGU
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Advancing Access to Global Flood Modeling and Alerting using the PDC DisasterAWARE Platform and Remote Sensing Technologies. Glasscoe, M., T.; Bausch, D., B.; Chiesa, C.; Hampe, G.; Tiampo, K., F.; Eguchi, R., T.; Huyck, C., K.; Pierce, M., E.; Wang, J.; Chen, Z.; Kar, B.; and Schumann, G. In American Geophysical Union Fall Meeting, 12 2019. AGU
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ManyClasses 1: Assessing the generalizable effect of immediate versus delayed feedback across many college classes. Fyfe, E.; Leeuw, J., d.; Carvalho, P.; Goldstone, R.; and Motz, B. Advances in Methods and Practices in Psychological Science. 2019.
doi   link   bibtex   abstract  
Rice Galaxy: an open resource for plant science. Juanillas, V.; Dereeper, A.; Beaume, N.; Droc, G.; Dizon, J.; Mendoza, J., R.; Perdon, J., P.; Mansueto, L.; Triplett, L.; Lang, J.; Zhou, G.; Ratharanjan, K.; Plale, B.; Haga, J.; Leach, J., E.; Ruiz, M.; Thomson, M.; Alexandrov, N.; Larmande, P.; Kretzschmar, T.; and Mauleon, R., P. , 8: 1-14. 2019.
Rice Galaxy: an open resource for plant science [pdf]Paper   Rice Galaxy: an open resource for plant science [link]Website   doi   link   bibtex   abstract  
The validity and utility of activity logs as a measure of student engagement. Motz, B.; Quick, J.; Schroeder, N.; Zook, J.; and Gunkel, M. In Proceedings of the 9th International Conference on Learning Analytics & Knowledge, pages 300-309, 3 2019. Association for Computing Machinery
The validity and utility of activity logs as a measure of student engagement [pdf]Paper   The validity and utility of activity logs as a measure of student engagement [link]Website   doi   link   bibtex   abstract  
Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics. Chang, P.; Allen, G.; Anderson, W.; Bianco, F., B.; Bloom, J., S.; Brady, P., R.; Brazier, A.; Cenko, S., B.; Couch, S., M.; DeYoung, T.; Deelman, E.; Etienne, Z., B.; Foley, R., J.; Fox, D., B.; Golkhou, V., Z.; Grant, D., R.; Hanna, C.; Holley-Bockelmann, K.; Howell, D., A.; Huerta, E., A.; Johnson, M., W., G.; Juric, M.; Kaplan, D., L.; Katz, D., S.; Keivani, A.; Kerzendorf, W.; Kopper, C.; Lam, M., T.; Lehner, L.; Marka, Z.; Marka, S.; Nabrzyski, J.; Narayan, G.; O'Shea, B., W.; Petravick, D.; Quick, R.; Street, R., A.; Taboada, I.; Timmes, F.; Turk, M., J.; Weltman, A.; and Zhang, Z. . 3 2019.
Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics [pdf]Paper   Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics [link]Website   link   bibtex   abstract  
Transparency by Design in eScience Research. Plale, B. In International Conference on eScience (eScience), pages 428-431, 3 2019. Institute of Electrical and Electronics Engineers (IEEE)
doi   link   bibtex   abstract  
Extending XSEDE Innovations to Campus Cyberinfrastructure - The XSEDE National Integration Toolkit. Coulter, E.; Sprouse, J.; Reynolds, R.; and Knepper, R. The Journal of Computational Science Education, 10(1): 16-20. 1 2019.
Extending XSEDE Innovations to Campus Cyberinfrastructure - The XSEDE National Integration Toolkit [pdf]Paper   Extending XSEDE Innovations to Campus Cyberinfrastructure - The XSEDE National Integration Toolkit [link]Website   doi   link   bibtex   abstract  
Jetstream (NSF Award 1445604) Annual Report: December 1, 2018 – November 28, 2019. Hancock, David Y; Merchant, Nirav; Lowe, John Michael; Fischer, Jeremy; Liming, Lee; Taylor, James; Afgan, Enis; Turner, George; Skidmore, Edwin; Beck, Brain W.; Snapp-Childs, Winona; Foster, Ian; Vaughn, M. Technical Report 2019.
Jetstream (NSF Award 1445604) Annual Report: December 1, 2018 – November 28, 2019 [link]Website   link   bibtex  
  2018 (69)
HarpLDA+: Optimizing latent dirichlet allocation for parallel efficiency. Peng, B.; Zhang, B.; Chen, L.; Avram, M.; Henschel, R.; Stewart, C.; Zhu, S.; McCallum, E.; Smith, L.; Zahniser, T.; Omer, J.; and Qiu, J. In Obradovic Z. Baeza-Yates R., K., J., N., R., W., C., T., M., S., T., H., X., C., A., B., R., T., J., Z., H., N., J., G., R., editor(s), Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017, volume 2018-Janua, pages 243-252, 2018. Institute of Electrical and Electronics Engineers Inc.
HarpLDA+: Optimizing latent dirichlet allocation for parallel efficiency [link]Website   doi   link   bibtex   abstract  
The Science Gateways Community Institute at Two Years. Wilkins-Diehr, N.; Zentner, M.; Pierce, M.; Dahan, M.; Lawrence, K.; Hayden, L.; and Mullinix, N. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-8, 7 2018. ACM Press
The Science Gateways Community Institute at Two Years [pdf]Paper   The Science Gateways Community Institute at Two Years [link]Website   doi   link   bibtex   abstract  
The CSBG - LSU Gateway. Abeysinghe, E.; Brylinski, M.; Christie, M.; Marru, S.; and Pierce, M. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
The CSBG - LSU Gateway [pdf]Paper   The CSBG - LSU Gateway [link]Website   doi   link   bibtex   abstract  
Apache Airavata Resource Allocation System: A Tool for Allocating Resources in Science Gateways. Phulwani, H.; Thapa, M.; Marru, S.; Pierce, M.; Pamidighantam, S.; and Christie, M. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 2018. ACM Press
Apache Airavata Resource Allocation System: A Tool for Allocating Resources in Science Gateways [pdf]Paper   Apache Airavata Resource Allocation System: A Tool for Allocating Resources in Science Gateways [link]Website   doi   link   bibtex   abstract  
Supporting Science Gateways Using Apache Airavata and SciGaP Services. Pierce, M.; Marru, S.; Abeysinghe, E.; Pamidighantam, S.; Christie, M.; and Wannipurage, D. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
Supporting Science Gateways Using Apache Airavata and SciGaP Services [pdf]Paper   Supporting Science Gateways Using Apache Airavata and SciGaP Services [link]Website   doi   link   bibtex   abstract  
Fracture Advancing Step Tectonics Observed in the Yuha Desert and Ocotillo, CA, Following the 2010 M w 7.2 El Mayor-Cucapah Earthquake. Donnellan, A.; Parker, J.; Heflin, M.; Lyzenga, G.; Moore, A.; Ludwig, L., G.; Rundle, J.; Wang, J.; and Pierce, M. Earth and Space Science, 5(9): 456-472. 9 2018.
Fracture Advancing Step Tectonics Observed in the Yuha Desert and Ocotillo, CA, Following the 2010 M w 7.2 El Mayor-Cucapah Earthquake [link]Website   doi   link   bibtex   abstract  
Evaluating NextCloud as a File Storage for Apache Airavata. Kariyattin, S.; Marru, S.; and Pierce, M. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
Evaluating NextCloud as a File Storage for Apache Airavata [pdf]Paper   Evaluating NextCloud as a File Storage for Apache Airavata [link]Website   doi   link   bibtex   abstract  
Scaling JupyterHub Using Kubernetes on Jetstream Cloud. Sarajlic, S.; Chastang, J.; Marru, S.; Fischer, J.; and Lowe, M. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
Scaling JupyterHub Using Kubernetes on Jetstream Cloud [pdf]Paper   Scaling JupyterHub Using Kubernetes on Jetstream Cloud [link]Website   doi   link   bibtex   abstract  
ImageX 3.0: a full stack imaging archive solution. Young, M., D.; Gopu, A.; and Perigo, R. In SPIE ASTRONOMICAL TELESCOPES + INSTRUMENTATION 10-15 June 2018 Austin, Texas, United States, pages 46, 7 2018. SPIE-Intl Soc Optical Eng
ImageX 3.0: a full stack imaging archive solution [pdf]Paper   doi   link   bibtex   abstract  
Scaling JupyterHub using Kubernetes on Jetstream cloud: Platform as a service for research and educational initiatives in the atmospheric sciences. Sarajlic, S.; Chastang, J.; Marru, S.; Fischer, J.; and Lowe, M. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), 7 2018. Association for Computing Machinery
Scaling JupyterHub using Kubernetes on Jetstream cloud: Platform as a service for research and educational initiatives in the atmospheric sciences [pdf]Paper   doi   link   bibtex   abstract  
Training children aged 5–10 years in compliance control: tracing smaller figures yields better learning not specific to the scale of drawn figures. Snapp-Childs, W.; Fath, A., J.; and Bingham, G., P. Experimental Brain Research, 236(10): 2589-2601. 10 2018.
Training children aged 5–10 years in compliance control: tracing smaller figures yields better learning not specific to the scale of drawn figures [pdf]Paper   doi   link   bibtex   abstract  
IQ-stations: Advances in state-of-the-art low cost immersive displays for research and development. Sherman, W., R.; Whiting, E.; Money, J., H.; and Grover, S. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), pages 5, 7 2018. Association for Computing Machinery
IQ-stations: Advances in state-of-the-art low cost immersive displays for research and development [pdf]Paper   doi   link   bibtex  
Limited mutation-rate variation within the Paramecium aurelia species complex. Long, H.; Doak, T., G.; and Lynch, M. G3: Genes, Genomes, Genetics, 8(7): 2523-2526. 7 2018.
Limited mutation-rate variation within the Paramecium aurelia species complex [pdf]Paper   doi   link   bibtex   abstract  
Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina. Zheng, W.; Wang, C.; Yan, Y.; Gao, F.; Doak, T., G.; and Song, W. Genome Biology and Evolution, 10(3): 883-894. 2018.
doi   link   bibtex   abstract  
Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. Yang, T.; Fang, L.; Sanders, S.; Jayanthi, S.; Rajan, G.; Podicheti, R.; Thallapuranam, S., K.; Mockaitis, K.; and Medina-Bolivar, F. The Journal of biological chemistry, 293(1): 28-46. 2018.
Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. [pdf]Paper   Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. [link]Website   doi   link   bibtex   abstract   1 download  
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution. Behringer, M., G.; Choi, B., I.; Miller, S., F.; Doak, T., G.; Karty, J., A.; Guo, W.; and Lynch, M. Proceedings of the National Academy of Sciences of the United States of America, 115(20): E4642-E4650. 2018.
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution [link]Website   doi   link   bibtex   abstract  
High Availability on Jetstream: Practices and Lessons Learned. Lowe, J., M.; Fischer, J.; Sudarshan, S.; Turner, G.; Stewart, C., A.; and Hancock, D., Y. In Proceedings of the 9th Workshop on Scientific Cloud Computing (ScienceCloud'18), of ScienceCloud'18, pages 4:1--4:7, 2018. ACM
High Availability on Jetstream: Practices and Lessons Learned [link]Website   doi   link   bibtex   abstract  
Methodologies and Practices for Adoption of a Novel National Research Environment. Fischer, J.; Beck, B., W.; Sudarshan, S.; Turner, G.; Snapp-Childs, W.; Stewart, C., A.; and Hancock, D., Y. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), of PEARC '18, pages 21:1--21:7, 2018. ACM
Methodologies and Practices for Adoption of a Novel National Research Environment [link]Website   doi   link   bibtex   abstract  
High Performance Photogrammetry for Academic Research. Ruan, G.; Wernert, E.; Sherman, W.; Gniady, T.; Tuna, E.; and Sherman, W. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), of PEARC '18, pages 45:1--45:8, 2018. ACM
High Performance Photogrammetry for Academic Research [link]Website   doi   link   bibtex   abstract  
A Computational Notebook Approach to Large-scale Text Analysis. Ruan, G.; Gniady, T.; Kloster, D.; Wernert, E.; and Tuna, E. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, of PEARC '18, pages 1-8, 2018. ACM Press
A Computational Notebook Approach to Large-scale Text Analysis [link]Website   doi   link   bibtex   abstract  
Toward sustainable deployment of distributed services on the cloud: dockerized ODI-PPA on Jetstream. Bao, Y.; Gopu, A.; Perigo, R.; and Young, M., D. In SPIE ASTRONOMICAL TELESCOPES + INSTRUMENTATION 10-15 June 2018 Austin, Texas, United States, pages 108, 7 2018. SPIE-Intl Soc Optical Eng
Toward sustainable deployment of distributed services on the cloud: dockerized ODI-PPA on Jetstream [pdf]Paper   doi   link   bibtex   abstract  
Data Capsule Appliance for Restricted Data in Libraries. Withana, S.; Kouper, I.; and Plale, B., A. In Workshop on Cyberinfrastructure and Machine Learning for Digital Libraries and Archives, in conjunction with Joint Conference on Digital Libraries 2018, 2018.
Data Capsule Appliance for Restricted Data in Libraries [link]Website   link   bibtex  
Subject headings and beyond: Mapping the HathiTrust Digital Library content for wider use. Edelblute, T.; Zoss, A.; and Kouper, I. In HathiTrust Research Center UnCamp 2018, 2018.
Subject headings and beyond: Mapping the HathiTrust Digital Library content for wider use [link]Website   link   bibtex  
Rice Galaxy: an open resource for plant science. Juanillas, V., M., J.; Dereeper, A.; Beaume, N.; Droc, G.; Dizon, J.; Mendoza, J., R.; Perdon, J., P.; Mansueto, L.; Triplett, L.; and Lang, J. bioRxiv,358754. 2018.
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Narrative visualization. Kouper, I. In 2018 Midwest Big Data Summer School, 2018.
Narrative visualization [link]Website   link   bibtex  
Restricted data types used in secure computing environments. Kouper, I.; and Mitchell, E. In HathiTrust Research Center UnCamp 2018, 2018.
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Harp-DAAL for High Performance Big Data Computing. Qiu, J. Parallel Universe. 3 2018.
Harp-DAAL for High Performance Big Data Computing [pdf]Paper   Harp-DAAL for High Performance Big Data Computing [pdf]Website   link   bibtex   abstract  
Structure of pion photoproduction amplitudes. Mathieu, V.; Nys, J.; Fernández-Ramírez, C.; Blin, A., H.; Jackura, A.; Pilloni, A.; Szczepaniak, A.; and Fox, G. Physical Review D, 98(1): 014041. 2018.
Structure of pion photoproduction amplitudes [link]Website   doi   link   bibtex  
Machine Learning for Parameter Auto-tuning in Molecular Dynamics Simulations: Efficient Dynamics of Ions near Polarizable Nanoparticles. Kadupitiya, J.; Fox, G., C.; and Jadhao, V. Technical Report 2018.
Machine Learning for Parameter Auto-tuning in Molecular Dynamics Simulations: Efficient Dynamics of Ions near Polarizable Nanoparticles [pdf]Paper   Machine Learning for Parameter Auto-tuning in Molecular Dynamics Simulations: Efficient Dynamics of Ions near Polarizable Nanoparticles [pdf]Website   doi   link   bibtex   abstract  
Vector meson photoproduction with a linearly polarized beam. Mathieu, V.; Nys, J.; Fernández-Ramírez, C.; Jackura, A.; Pilloni, A.; Sherrill, N.; Szczepaniak, A., P.; and Fox, G. Physical Review D, 97(9). 2018.
Vector meson photoproduction with a linearly polarized beam [link]Website   doi   link   bibtex   abstract  
Crossover analysis and automated layer-tracking assessment of the extracted DEM of the basal topography of the canadian arctic archipelago ice-cap. Al-Ibadi, M.; Sprick, J.; Athinarapu, S.; Berger, V.; Stumpf, T.; Paden, J.; Leuschen, C.; Rodriguez, F.; Xu, M.; Crandall, D.; Fox, G.; Burgess, D.; Sharp, M.; Copland, L.; and Van Wychen, W. 2018 IEEE Radar Conference, RadarConf 2018,862-867. 2018.
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Performance Characterization of Multi-threaded Graph Processing Applications on Intel Many-Integrated-Core Architecture. Liu, X.; Chen, L.; Firoz, J., S.; Qiu, J.; and Jiang, L. In 2018 IEEE International Symposium on Performance Analysis of Systems and Software, ISPASS 2018, pages 199–208, 2018. Institute of Electrical and Electronics Engineers Inc.
Performance Characterization of Multi-threaded Graph Processing Applications on Intel Many-Integrated-Core Architecture [link]Website   doi   link   bibtex   abstract  
Object Detection by a Super-Resolution Method and a Convolutional Neural Networks. Na, B.; and Fox, G., C. In 2018 IEEE International Conference on Big Data, Big Data, pages 2263-2269, 1 2018. Institute of Electrical and Electronics Engineers Inc.
Object Detection by a Super-Resolution Method and a Convolutional Neural Networks [pdf]Paper   doi   link   bibtex   abstract  
Evaluating the scientific impact of XSEDE. Wang, F.; Fox, G., C.; Von Laszewski, G.; Furlani, T., R.; Gallo, S., M.; Whitson, T.; and DeLeon, R., L. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), 7 2018. Association for Computing Machinery
Evaluating the scientific impact of XSEDE [pdf]Paper   doi   link   bibtex   abstract  
Evaluation of Production Serverless Computing Environments. Lee, H.; Satyam, K.; and Fox, G. In IEEE International Conference on Cloud Computing, CLOUD, volume 2018-July, pages 442-450, 9 2018. IEEE Computer Society
Evaluation of Production Serverless Computing Environments [pdf]Paper   doi   link   bibtex   abstract  
Automated tracking of 2D and 3D ice radar imagery using Viterbi and TRW-S. Berger, V.; Xu, M.; Chu, S.; Crandall, D.; Paden, J.; and Fox, G., C. In International Geoscience and Remote Sensing Symposium (IGARSS), volume 2018-July, pages 4162-4165, 10 2018. Institute of Electrical and Electronics Engineers Inc.
Automated tracking of 2D and 3D ice radar imagery using Viterbi and TRW-S [pdf]Paper   doi   link   bibtex   abstract  
Finding and counting tree-like subgraphs using MapReduce. Zhao, Z.; Chen, L.; Avram, M.; Li, M.; Wang, G.; Butt, A.; Khan, M.; Marathe, M.; Qiu, J.; and Vullikanti, A. IEEE Transactions on Multi-Scale Computing Systems, 4(3): 217-230. 7 2018.
Finding and counting tree-like subgraphs using MapReduce [link]Website   doi   link   bibtex   abstract  
Deep hybrid wavelet network for ice boundary detection in radra imagery. Kamangir, H.; Rahnemoonfar, M.; Dobbs, D.; Paden, J.; and Fox, G. In International Geoscience and Remote Sensing Symposium (IGARSS), volume 2018-July, pages 3449-3452, 10 2018. Institute of Electrical and Electronics Engineers Inc.
Deep hybrid wavelet network for ice boundary detection in radra imagery [pdf]Paper   doi   link   bibtex   abstract  
Big Data Benchmarks on Bare Metal Cloud. Lee, H.; and Fox, G., C. Technical Report 2018.
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Big data and extreme-scale computing: Pathways to Convergence-Toward a shaping strategy for a future software and data ecosystem for scientific inquiry. Asch, M.; Moore, T.; Badia, R.; Beck, M.; Beckman, P.; Bidot, T.; Bodin, F.; Cappello, F.; Choudhary, A.; de Supinski, B.; Deelman, E.; Dongarra, J.; Dubey, A.; Fox, G.; Fu, H.; Girona, S.; Gropp, W.; Heroux, M.; Ishikawa, Y.; Keahey, K.; Keyes, D.; Kramer, W.; Lavignon, J., F.; Lu, Y.; Matsuoka, S.; Mohr, B.; Reed, D.; Requena, S.; Saltz, J.; Schulthess, T.; Stevens, R.; Swany, M.; Szalay, A.; Tang, W.; Varoquaux, G.; Vilotte, J., P.; Wisniewski, R.; Xu, Z.; and Zacharov, I. Volume 32 2018.
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Task Scheduling in Big Data - Review, Research Challenges, and Prospects. Govindarajan, K.; Kamburugamuve, S.; Wickramasinghe, P.; Abeykoon, V.; and Fox, G. In 2017 9th International Conference on Advanced Computing, ICoAC 2017, pages 165-173, 8 2018. Institute of Electrical and Electronics Engineers Inc.
Task Scheduling in Big Data - Review, Research Challenges, and Prospects [pdf]Paper   doi   link   bibtex   abstract   1 download  
Features of πΔ photoproduction at high energies. Nys, J.; Mathieu, V.; Fernández-Ramírez, C.; Jackura, A.; Mikhasenko, M.; Pilloni, A.; Sherrill, N.; Ryckebusch, J.; Szczepaniak, A., P.; Fox, G., C.; and Center, J., P., A. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, 779: 77-81. 2018.
Features of πΔ photoproduction at high energies [link]Website   doi   link   bibtex   abstract  
Analyticity Constraints for Hadron Amplitudes: Going High to Heal Low Energy Issues. Mathieu, V.; Nys, J.; Pilloni, A.; Fernández-Ramírez, C.; Jackura, A.; Mikhasenko, M.; Pauk, V.; Szczepaniak, A., P.; and Fox, G. Europhysics Letters, 122(4): 41001-p1-p5. 2018.
Analyticity Constraints for Hadron Amplitudes: Going High to Heal Low Energy Issues [link]Website   link   bibtex   abstract  
Contributions to High-Performance Big Data Computing. Fox, G.; Qiu, J.; Crandall, D.; Laszewski, G., V.; Beckstein, O.; Paden, J.; Paraskevakos, I.; Jha, S.; Wang, F.; Marathe, M.; Vullikanti, A.; and Cheatham, T. Technical Report 2018.
Contributions to High-Performance Big Data Computing [pdf]Paper   Contributions to High-Performance Big Data Computing [link]Website   link   bibtex   abstract  
Detecting ice layers in radar images with deep learning. Hamid Kamangir, Maryam Rahnemoonfar, Dugan Dobbs, J Paden, G., F. Technical Report 2018.
Detecting ice layers in radar images with deep learning [pdf]Website   link   bibtex   abstract  
Multi-task Spatiotemporal Neural Networks for Structured Surface Reconstruction. Xu, M.; Fan, C.; Paden, J., D.; Fox, G., C.; and Crandall, D., J. In Proceedings - 2018 IEEE Winter Conference on Applications of Computer Vision, WACV 2018, volume 2018-Janua, pages 1273-1282, 5 2018. Institute of Electrical and Electronics Engineers Inc.
Multi-task Spatiotemporal Neural Networks for Structured Surface Reconstruction [pdf]Paper   doi   link   bibtex   abstract  
Twister: Net - Communication Library for Big Data Processing in HPC and Cloud Environments. Kamburugamuve, S.; Wickramasinghe, P.; Govindarajan, K.; Uyar, A.; Gunduz, G.; Abeykoon, V.; and Fox, G. In IEEE International Conference on Cloud Computing, CLOUD, volume 2018-July, pages 383-391, 9 2018. IEEE Computer Society
Twister: Net - Communication Library for Big Data Processing in HPC and Cloud Environments [pdf]Paper   doi   link   bibtex   abstract  
Global analysis of charge exchange meson production at high energies. Nys, J.; Hiller Blin, A., N.; Mathieu, V.; Fernández-Ramírez, C.; Jackura, A.; Pilloni, A.; Ryckebusch, J.; Szczepaniak, A., P.; and Fox, G. . 2018.
Global analysis of charge exchange meson production at high energies [pdf]Paper   doi   link   bibtex   abstract  
Task-parallel analysis of molecular dynamics trajectories. Paraskevakos, I.; Chantzialexiou, G.; Luckow, A.; Cheatham, T., E.; Khoshlessan, M.; Beckstein, O.; Fox, G., C.; and Jha, S. In Proceedings of the 47th International Conference on Parallel Processing (ICPP 2018), 8 2018. Association for Computing Machinery
Task-parallel analysis of molecular dynamics trajectories [pdf]Paper   doi   link   bibtex   abstract  
Searching the Sequence Read Archive Using Jetstream and Wrangler. Levi, K.; Rynge, M.; Abeysinghe, E.; and Edwards, R., A. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), of PEARC '18, pages 50:1--50:7, 7 2018. ACM
Searching the Sequence Read Archive Using Jetstream and Wrangler [pdf]Paper   Searching the Sequence Read Archive Using Jetstream and Wrangler [link]Website   doi   link   bibtex   abstract  
Grid Technology for Supporting Health Education and Measuring the Health Outcome. Sukhija, N.; Datta, A., K.; Sevin, S.; Coulter, E.; Datta, A., K.; and Coulter, E. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), of PEARC '18, pages 89:1--89:4, 7 2018. ACM
Grid Technology for Supporting Health Education and Measuring the Health Outcome [pdf]Paper   Grid Technology for Supporting Health Education and Measuring the Health Outcome [link]Website   doi   link   bibtex   abstract  
Jetstream—Early operations performance, adoption, and impacts. Hancock, D., Y.; Stewart, C., A.; Vaughn, M.; Fischer, J.; Lowe, J., M.; Turner, G.; Swetnam, T., L.; Chafin, T., K.; Afgan, E.; Pierce, M., E.; Snapp‐Childs, W.; and Snapp-Childs, W. Concurrency and Computation: Practice and Experience. 9 2018.
Jetstream—Early operations performance, adoption, and impacts [pdf]Paper   Jetstream—Early operations performance, adoption, and impacts [link]Website   doi   link   bibtex   abstract   1 download  
The Report of the 2018 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure. Andrew Adams, Jeannette Dopheide, Mark Krenz, James Marsteller, V., W.; and and John Zage Technical Report 2018.
The Report of the 2018 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure [pdf]Paper   The Report of the 2018 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure [link]Website   link   bibtex  
Trusted CI Annual Report for 2018. Adams, A.; Avila, K.; Atkins, J.; Basney, J.; Bohland, L.; Borecky, D.; Cowles, R.; Dopheide, J.; Fleury, T.; Harbour, G.; Heymann, E.; Hudson, F.; Jackson, C.; Kiser, R.; Krenz, M.; Marsteller, J.; Miller, B.; Raquel, W.; Ruff, P.; Russell, S.; Shah, Z.; Shankar, A.; Sons, S.; Welch, V.; and Zage, J. Technical Report 2018.
Trusted CI Annual Report for 2018 [pdf]Paper   Trusted CI Annual Report for 2018 [link]Website   link   bibtex  
A New Science Gateway to Provide Decision Support on Carbon Capture and Storage Technologies. Wang, Y.; Pamidighantam, S.; Yaw, S.; Abeysinghe, E.; Marru, S.; Christie, M.; Ellett, K.; Pierce, M.; and Middleton, R. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, of PEARC '18, pages 1-3, 2018. ACM Press
A New Science Gateway to Provide Decision Support on Carbon Capture and Storage Technologies [link]Website   doi   link   bibtex   abstract  
Science Gateway Implementation at the University of South Dakota. Madison, J., D.; Abeysinghe, E.; Pamidighantam, S.; Marru, S.; Christie, M.; Jennewein, D., M.; and Pierce, M. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
Science Gateway Implementation at the University of South Dakota [pdf]Paper   Science Gateway Implementation at the University of South Dakota [link]Website   doi   link   bibtex   abstract  
Django Content Management System Evaluation and Integration with Apache Airavata. Adithela, S., P.; Christie, M.; Marru, S.; and Pierce, M. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
Django Content Management System Evaluation and Integration with Apache Airavata [pdf]Paper   Django Content Management System Evaluation and Integration with Apache Airavata [link]Website   doi   link   bibtex   abstract  
Radar Determination of Fault Slip and Location in Partially Decorrelated Images. Parker, J.; Glasscoe, M.; Donnellan, A.; Stough, T.; Pierce, M.; and Wang, J. Earthquakes and Multi-hazards Around the Pacific Rim, Vol. I, pages 101-116. Springer, 2018.
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Your Good Health is a Workforce Issue. Stewart, C., A.; and Krefeldt, M. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), of PEARC '18, pages 75:1--75:8, 2018. ACM
Your Good Health is a Workforce Issue [link]Website   doi   link   bibtex   abstract  
Using a Science Gateway to Deliver SimVascular Software As a Service for Classroom Instruction. Wilson, N., M.; Marru, S.; Abeysinghe, E.; Christie, M., A.; Maher, G., D.; Updegrove, A., R.; Pierce, M.; and Marsden, A., L. In Proceedings of the Practice and Experience on Advanced Research Computing, of PEARC '18, pages 102:1--102:4, 2018. ACM
Using a Science Gateway to Deliver SimVascular Software As a Service for Classroom Instruction [link]Website   doi   link   bibtex   abstract  
PHASTA Science Gateway for High Performance Computational Fluid Dynamics. Smith, C., W.; Abeysinghe, E.; Marru, S.; and Jansen, K., E. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, pages 1-4, 7 2018. ACM Press
PHASTA Science Gateway for High Performance Computational Fluid Dynamics [pdf]Paper   PHASTA Science Gateway for High Performance Computational Fluid Dynamics [link]Website   doi   link   bibtex   abstract  
Simplifying Access to Campus Resources at Southern Illinois University with a Science Gateway. Sunkara, S., S.; Langin, C.; Pierce, M.; Abeysinghe, E.; Pamidighantam, S.; and Marru, S. In Proceedings of the Practice and Experience on Advanced Research Computing - PEARC '18, of PEARC '18, pages 1-4, 2018. ACM Press
Simplifying Access to Campus Resources at Southern Illinois University with a Science Gateway [link]Website   doi   link   bibtex   abstract  
Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata. Wang, Z.; Christie, M., A.; Abeysinghe, E.; Chu, T.; Marru, S.; Pierce, M.; and Danko, C., G. In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18), of PEARC '18, pages 39:1--39:7, 2018. ACM
Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata [link]Website   doi   link   bibtex   abstract  
Big provenance stream processing for data intensive computations. Suriarachchi, I.; Withana, S.; and Plale, B. In Proceedings - IEEE 14th International Conference on eScience, e-Science 2018, pages 245-255, 12 2018. Institute of Electrical and Electronics Engineers Inc.
doi   link   bibtex   abstract  
ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report. Doak, T., G.; Stewart, C., A.; and Michaels, S., D. Technical Report 9 2018.
ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report [pdf]Paper   ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report [link]Website   link   bibtex   abstract  
Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop. Sanders, S., A.; Ganote, C., L.; Papudeshi, B.; Stewart, C., A.; and Doak, T., G. Technical Report 6 2018.
Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop [pdf]Paper   Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop [link]Website   link   bibtex   abstract  
  2017 (70)
Hybrid Supervised-unsupervised Image Topic Visualization with Convolutional Neural Network and LDA. Zhen, K.; Birla, M.; Crandall, D.; Zhang, B.; and Qiu, J. arXiv preprint arXiv:1703.05243. 2017.
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Teaching, Learning and Collaborating through Cloud Computing Online Classes. Qiu, J.; Kamburugamuve, S.; Lee, H.; Mitchell, J.; Caldwell, R.; Bullock, G.; and Hayden, L. In EduHPC'17 workshop at SC17, 2017.
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Harp-DAAL: A High Performance Data-Intensive Machine Learning Framework. Chen, L.; and Qiu, J. Technical Report 2017.
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Parallelizing Big Data Machine Learning Applications with Model Rotation. Zhang, B.; Peng, B.; and Qiu, J. ser. Advances in Parallel Computing. 2017.
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A Survey: Runtime Software Systems for High Performance Computing. Sterling, T.; Anderson, M.; and Brodowicz, M. Supercomputing Frontiers and Innovations, 4(1): 48-68. 2017.
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Simultac Fonton: A Fine-Grain Architecture for Extreme Performance beyond Moore's Law. Brodowicz, M.; and Sterling, T. Supercomputing Frontiers and Innovations, 4(2): 27-37. 2017.
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Asymptotic Computing–Undoing the Damage. STERLING, T.; BRODOWICZ, M.; and KOGLER, D. New Frontiers in High Performance Computing and Big Data, 30: 55. 2017.
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Declarative Guide Creation. Cottam, J., A.; and Lumsdaine, A. Electronic Imaging, 2017(1): 22-33. 2017.
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High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. Ozik, J.; Collier, N.; Wozniak, J.; Macal, C.; Cockrell, C.; Friedman, S.; Ghaffarizadeh, A.; Heiland, R.; An, G.; and Macklin, P. bioRxiv,196709. 2017.
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QuakeSim lessons for NASA Earth Science sensor webs. Parker, J.; Donnellan, A.; and Pierce, M. Technical Report 2017.
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Better Data Discoverability in Science Gateways. Nakandala, S.; Pamidighantam, S.; Marru, S.; and Pierce, M. In Science Gateways, 2017.
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Science gateways incubator: Software sustainability meets community needs. Gesing, S.; Zentner, M.; Casavan, J.; Hillery, B.; Vorvoreanu, M.; Heiland, R.; Marru, S.; Pierce, M.; Mullinix, N.; and Maron, N. In Proceedings - 13th IEEE International Conference on eScience, eScience 2017, pages 477-485, 11 2017. Institute of Electrical and Electronics Engineers Inc.
Science gateways incubator: Software sustainability meets community needs [pdf]Paper   doi   link   bibtex   abstract  
The PHASTA Science Gateway. Smith, C., W.; and Abeysinghe, E. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact - PEARC17, volume Part F1287, pages 1-4, 7 2017. ACM Press
The PHASTA Science Gateway [pdf]Paper   The PHASTA Science Gateway [link]Website   doi   link   bibtex   abstract  
Diversity and universality of endosymbiotic Rickettsia in the fish parasite Ichthyophthirius multifiliis. Zaila, K., E.; Doak, T., G.; Ellerbrock, H.; Tung, C.; Martins, M., L.; Kolbin, D.; Yao, M.; Cassidy-Hanley, D., M.; Clark, T., G.; and Chang, W. Frontiers in Microbiology, 8(FEB): 189. 2017.
Diversity and universality of endosymbiotic Rickettsia in the fish parasite Ichthyophthirius multifiliis [link]Website   doi   link   bibtex   abstract   2 downloads  
Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis. Klegarth, A., R.; Sanders, S., A.; Gloss, A., D.; Lane‐deGraaf, K., E.; Jones‐Engel, L.; Fuentes, A.; and Hollocher, H. American Journal of Physical Anthropology. 2017.
Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis [link]Website   doi   link   bibtex  
Population Genomics of Paramecium Species. Johri, P.; Krenek, S.; Marinov, G., K.; Doak, T., G.; Berendonk, T., U.; and Lynch, M. Molecular Biology and Evolution, 34(5): 1194-1216. 2017.
Population Genomics of Paramecium Species [link]Website   doi   link   bibtex   abstract  
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes. Papudeshi, B.; Haggerty, J., M.; Doane, M.; Morris, M., M.; Walsh, K.; Beattie, D., T.; Pande, D.; Zaeri, P.; Silva, G., G.; Thompson, F.; Edwards, R., A.; and Dinsdale, E., A. BMC Genomics, 18(1). 2017.
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes [pdf]Paper   Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes [link]Website   doi   link   bibtex   abstract  
Estimating seven coefficients of pairwise relatedness using population-genomic data. Ackerman, M., S.; Johri, P.; Spitze, K.; Xu, S.; Doak, T., G.; Young, K.; and Lynch, M. Genetics, 206(1): 105-118. 2017.
Estimating seven coefficients of pairwise relatedness using population-genomic data [link]Website   doi   link   bibtex   abstract  
A voice for bioinformatics. Ganote, C., L.; Sanders, S., A.; Papudeshi, B., N.; Blood, P., D.; and Doak, T., G. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, 2017. Association for Computing Machinery
A voice for bioinformatics [link]Website   doi   link   bibtex   abstract  
Scalable photogrammetry with high performance computing. Gniady, T.; Ruan, G.; Sherman, W.; Tuna, E.; and Wernert, E. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, pages 3, 2017. Association for Computing Machinery
Scalable photogrammetry with high performance computing [link]Website   doi   link   bibtex   abstract  
Jetstream: A Cloud System Enabling Learning in Higher Education Communities. Fischer, J.; Hancock, D., Y.; Lowe, J., M.; Turner, G.; Snapp-Childs, W.; and Stewart, C., A. In Proceedings of the 2017 ACM SIGUCCS Annual Conference, volume Part F1317, pages 67-72, 10 2017. ACM
Jetstream: A Cloud System Enabling Learning in Higher Education Communities [pdf]Paper   Jetstream: A Cloud System Enabling Learning in Higher Education Communities [link]Website   doi   link   bibtex   abstract  
Performance Benchmarking of the R Programming Environment on the Stampede 1 . 5 Supercomputer. Mccombs, J., R.; and Michael, S. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, pages 8, 2017. Association for Computing Machinery
Performance Benchmarking of the R Programming Environment on the Stampede 1 . 5 Supercomputer [link]Website   doi   link   bibtex   abstract  
High performance computing enabled simulation of the food-water-energy system. Dennis, H., E., B.; Ward, A., S.; Balson, T.; Li, Y.; Henschel, R.; Slavin, S.; Simms, S.; and Brunst, H. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, pages 10, 2017. Association for Computing Machinery
High performance computing enabled simulation of the food-water-energy system [link]Website   doi   link   bibtex   abstract  
Summary of the 2017 NCGAS User Survey. Doak, T., G.; Stewart, C., A.; and Michaels, S., D. Technical Report 2017.
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ABI Sustaining: The National Center for Genome Analysis Support 2017 Annual Report. Doak, T., G.; Stewart, C., A.; and Michaels, S., D. Technical Report 2017.
ABI Sustaining: The National Center for Genome Analysis Support 2017 Annual Report [link]Website   link   bibtex  
Forward Observer system for radar data workflows: Big data management in the field. Knepper, R.; and Standish, M. Future Generation Computer Systems, 76: 92-97. 2017.
Forward Observer system for radar data workflows: Big data management in the field [link]Website   doi   link   bibtex   abstract  
Campus Compute Co-operative (CCC): A service oriented cloud federation. Grimshaw, A.; Prodhan, M.; Thomas, A.; Stewart, C.; and Knepper, R. In Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, 2017.
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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. Haas, B.; Dobin, A.; Stransky, N.; Li, B.; Yang, X.; Tickle, T.; Bankapur, A.; Ganote, C.; Doak, T.; and Pochet, N. bioRxiv,120295. 2017.
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Jetstream: Early Operations Performance, Adoption, and Impacts. Hancock, D. In Proceedings of the10th International Conference on Utility and Cloud Computing, of UCC '17, pages 7, 2017. ACM
Jetstream: Early Operations Performance, Adoption, and Impacts [link]Website   doi   link   bibtex  
Addressing the national need for more diversity and aggregate investment in cyberinfrastructure supporting open science and engineering research. Stewart, C., A. Technical Report 2017.
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XDMoD value analytics: A tool for measuring the financial and intellectual ROI of your campus cyberinfrastructure facilities. Fulton, B.; Gallo, S.; Henschel, R.; Yearke, T.; Börner, K.; DeLeon, R., L.; Furlani, T.; Stewart, C., A.; and Link, M. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17 ), volume Part F1287, pages 7, 7 2017. Association for Computing Machinery
XDMoD value analytics: A tool for measuring the financial and intellectual ROI of your campus cyberinfrastructure facilities [pdf]Paper   XDMoD value analytics: A tool for measuring the financial and intellectual ROI of your campus cyberinfrastructure facilities [link]Website   doi   link   bibtex   abstract  
A hybrid approach to population construction for agricultural agent-based simulation. Chen, P.; Evans, T.; Frisby, M.; Izquierdo, E.; and Plale, B. In Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, 2017.
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The Centrality of Data: Data Lifecycle and Data Pipelines. Plale, B.; and Kouper, I. Data Analytics for Intelligent Transportation Systems, pages 91-111. Elsevier, 2017.
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Low latency stream processing: Apache Heron with Infiniband & Intel Omni-Path. Kamburugamuve, S.; Ramasamy, K.; Swany, M.; and rey Fox, G. In UCC, 2017.
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Enhancing access to digital media: The language application grid in the HTRC Data Capsule. Pustejovsky, J.; Verhagen, M.; Rim, K.; Ma, Y.; Ran, L.; Liyanage, S.; Murdock, J.; McDonald, R.; and Plale, B. In ACM International Conference Proceeding Series, volume Part F1287, 2017.
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Pacific Rim Applications and Grid Middleware Assembly (PRAGMA): International clouds for data science. Plale, B.; and Chen, M. Concurrency Computation, 29(13). 2017.
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Towards Publishing Secure Capsule-Based Analysis. Murdock, J.; Jett, J.; Cole, T.; Ma, Y.; Downie, J.; and Plale, B. In Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, 2017.
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Data Capsule Appliance for Research Analysis of Restricted and Sensitive Data in Academic Libraries. McDonald, R., H.; Mitchell, E.; Unsworth, J.; and Kouper, I. In Coalition of Networked Information Fall Meeting CNI-2017, 2017.
Data Capsule Appliance for Research Analysis of Restricted and Sensitive Data in Academic Libraries [link]Website   link   bibtex  
Comet - Tales from the Long Tail - Two years in and 10,000 users later. Strandea, S.; Caia, H.; Cooper, T.; Flammer, K.; Irving, C.; Von Laszewski, G.; Majumdar, A.; Mishin, D.; Papadopoulos, P.; Pfeiffer, W.; Sinkovits, R.; Tatineni, M.; Wagner, R.; Wang, F.; Wilkins-Diehr, N.; Wolter, N.; and Norman, M. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, 2017.
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Provenance Enriched PID Kernel Information as OAI-ORE Map Replacement for SEAD Research Objects. Kouper, I.; Luo, Y.; Suriarachchi, I.; and Plale, B. In Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, 2017.
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Offloading Collective Operations to Programmable Logic. Arap, O.; Brasilino, L.; Kissel, E.; Shroyer, A.; and Swany, M. IEEE Micro, 37(5). 2017.
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OSiRIS: a distributed Ceph deployment using software defined networking for multi-institutional research. McKee, S.; Kissel, E.; Meekhof, B.; Swany, M.; Miller, C.; and Gregorowicz, M. In Journal of Physics: Conference Series, volume 898, pages 62045, 2017. IOP Publishing
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Identification and characterization of information-networks in long-tail data collections. Elag, M.; Kumar, P.; Marini, L.; Myers, J.; Hedstrom, M.; and Plale, B. Environmental Modelling and Software, 94. 2017.
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High-Performance Massive Subgraph Counting Using Pipelined Adaptive-Group Communication. Chen, L.; Peng, B.; Ossen, S.; Vullikanti, A.; Marathe, M.; Jiang, L.; and Qiu, J. In Big Data and HPC: Ecosystem and Convergence, TopHPC 2017, pages 173-197, 2017.
High-Performance Massive Subgraph Counting Using Pipelined Adaptive-Group Communication. [link]Website   doi   link   bibtex   abstract  
Mining lake time series using symbolic representation. Ruan, G.; Hanson, P., C.; Dugan, H.; and Plale, B., A. Ecological Informatics, 39. 2017.
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Low Latency Stream Processing: Twitter Heron with Infiniband and Omni-Path. Kamburugamuve, S.; Ramasamy, K.; Swany, M.; and Fox, G., C. In Proceedings of Strata Data Conference, 2017.
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Introduction to Harp: when Big Data Meets HPC. Zhang, B.; Peng, B.; Chen, L.; Li, E.; Zhou, Y.; and Qiu, J. Technical Report 2017.
Introduction to Harp: when Big Data Meets HPC [pdf]Paper   Introduction to Harp: when Big Data Meets HPC [link]Website   link   bibtex   abstract  
SERVOGrid Technical Documentation. Aktas, M.; Aydin, G.; Fox, G., C.; Gadgil, H.; Pierce, M.; Sayar, A.; McLeod, D.; and Sung, S. Technical Report 2017.
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Science Gateways: Sustainability via On-Campus Teams. Gesing, S.; Lawrence, K.; Wilkins-Diehr, N.; Dahan, M.; Zentner, M.; and Pierce, M., E. In Gateways 2017, volume 94, pages 97-102, 5 2017. Elsevier B.V.
Science Gateways: Sustainability via On-Campus Teams [pdf]Paper   Science Gateways: Sustainability via On-Campus Teams [link]Website   doi   link   bibtex   abstract  
Science Gateways: The Long Road to the Birth of an Institute. Gesing, S.; Wilkins-Diehr, N.; Dahan, M.; Lawrence, K.; Zentner, M.; Pierce, M.; Hayden, L.; and Marru, S. In Proceedings of the 50th Hawaii International Conference on System Sciences (2017), pages 10 pages, 2017. Hawaii International Conference on System Sciences
Science Gateways: The Long Road to the Birth of an Institute [pdf]Paper   Science Gateways: The Long Road to the Birth of an Institute [link]Website   doi   link   bibtex   abstract  
Bulk Collection: Systematic Government Access to Private-Sector Data. Cate, F., H.; and Dempsey, J., X. Oxford University Press, 2017.
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Machine Learning with Personal Data: Is Data Protection Law Smart Enough to Meet the Challenge?. Cate, F., H.; Kuner, C.; Svantesson, D., J., B.; Lynskey, O.; and Millard, C. International Data Privacy Law, 7(1): 1-2. 2017.
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The medical science DMZ: a network design pattern for data-intensive medical science. Peisert, S.; Dart, E.; Barnett, W.; Balas, E.; Cuff, J.; Grossman, R., L.; Berman, A.; Shankar, A.; and Tierney, B. Journal of the American Medical Informatics Association. 2017.
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The Rise of Cybersecurity and Its Impact on Data Protection. Cate, F., H.; Kuner, C.; Svantesson, D., J., B.; Lynskey, O.; and Millard, C. International Data Privacy Law, 7(2): 73-75. 2017.
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Apache airavata sharing service: A tool for enabling user collaboration in science gateways. Nakandala, S.; Marru, S.; Piece, M.; Pamidighantam, S.; Yoshimoto, K.; Schwartz, T.; Sivagnanam, S.; Majumdar, A.; and Miller, M., A. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, 7 2017. Association for Computing Machinery
Apache airavata sharing service: A tool for enabling user collaboration in science gateways [pdf]Paper   doi   link   bibtex   abstract  
A Non-Natural Wurtzite Polymorph of HgSe: A Potential 3D Topological Insulator. Dumett Torres, D.; Banerjee, P.; Pamidighantam, S.; and Jain, P., K. Chemistry of Materials, 29(15): 6356-6366. 8 2017.
A Non-Natural Wurtzite Polymorph of HgSe: A Potential 3D Topological Insulator [pdf]Paper   A Non-Natural Wurtzite Polymorph of HgSe: A Potential 3D Topological Insulator [link]Website   doi   link   bibtex   abstract  
Radar Determination of Fault Slip and Location in Partially Decorrelated Images. Parker, J.; Glasscoe, M.; Donnellan, A.; Stough, T.; Pierce, M.; and Wang, J. Pure and Applied Geophysics, 174(6): 2295-2310. 2017.
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Stampede 2: The Evolution of an XSEDE supercomputer. Stanzione, D.; Barth, B.; Gaffney, N.; Gaither, K.; Mehringer, S.; Hempel, C.; Wernert, E.; Minyard, T.; Tufo, H.; Panda, D.; and Teller, P. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, pages 8, 2017. Association for Computing Machinery
Stampede 2: The Evolution of an XSEDE supercomputer [link]Website   doi   link   bibtex   abstract  
An archive of spectra from the Mayall Fourier transform spectrometer at Kitt Peak. Pilachowski, C., A.; Hinkle, K., H.; Young, M., D.; Dennis, H., B.; Gopu, A.; Henschel, R.; and Hayashi, S. Publications of the Astronomical Society of the Pacific, 129(972). 2017.
An archive of spectra from the Mayall Fourier transform spectrometer at Kitt Peak [link]Website   doi   link   bibtex   abstract  
The Open Science Cyber Risk Profile: The Rosetta Stone for Open Science and Cybersecurity. Peisert, S.; and Welch, V. IEEE Security and Privacy, 15(5): 94-95. 2017.
The Open Science Cyber Risk Profile: The Rosetta Stone for Open Science and Cybersecurity [link]Website   doi   link   bibtex   abstract  
Using the Jetstream Research Cloud to provide Science Gateway resources. Knepper, R.; Coulter, E.; Pierce, M.; Marru, S.; and Pamidighantam, S. In Proceedings of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid '17), pages 753-757, 5 2017. IEEE
Using the Jetstream Research Cloud to provide Science Gateway resources [link]Website   doi   link   bibtex   abstract  
Indiana University Pervasive Technology Institute. Stewart, C., A.; Welch, V.; Plale, B.; Fox, G., C.; Pierce, M.; and Sterling, T. Technical Report 2017.
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One network metric datastore to track them all: the OSG network metric service. Quick, R.; Babik, M.; Fajardo, E., M.; Gross, K.; Hayashi, S.; Krenz, M.; Lee, T.; Mckee, S.; Pipes, C.; and Teige, S. Journal of Physics: Conf. Series, 898: 82044. 2017.
One network metric datastore to track them all: the OSG network metric service [pdf]Paper   doi   link   bibtex   abstract  
Benchmarking Harp-DAAL: High Performance Hadoop on KNL Clusters. Chen, L.; Peng, B.; Zhang, B.; Liu, T.; Zou, Y.; Jiang, L.; Henschel, R.; Stewart, C.; Zhang, Z.; McCallum, E.; Tom, Z.; Jon, O.; and Qiu, J. In 2017 IEEE 10th International Conference on Cloud Computing (CLOUD), volume 2017-June, pages 82-89, 6 2017. IEEE
Benchmarking Harp-DAAL: High Performance Hadoop on KNL Clusters [link]Website   doi   link   bibtex   abstract  
Jetstream Stakeholder Advisory Board Meeting February 2017: Presenters' Report. Stewart, C., A.; Hancock, D., Y.; Vaughn, M.; Merchant, N.; Lowe, J., M.; Fischer, J.; Liming, L.; Taylor, J.; Turner, G.; Hammond, C., B.; Skidmore, E.; Packard, M.; Miller, T.; Foster, I.; Rad, P.; and Mehringer, S. Technical Report 2 2017.
Jetstream Stakeholder Advisory Board Meeting February 2017: Presenters' Report [link]Website   link   bibtex  
Jetstream (NSF Award 1445604) Year Program Year 3 Annual Report (December 1, 2016 – November 28, 2017). Stewart, C., A.; Hancock, D., Y.; Vaughn, M.; Merchant, N.; Fischer, J.; Michael Lowe, J.; Liming, L.; Taylor, J.; Afgan, E.; Turner, G.; Skidmore, E.; Packard, M.; Beck, B., W.; and Foster, I. Technical Report 12 2017.
Jetstream (NSF Award 1445604) Year Program Year 3 Annual Report (December 1, 2016 – November 28, 2017) [pdf]Paper   Jetstream (NSF Award 1445604) Year Program Year 3 Annual Report (December 1, 2016 – November 28, 2017) [link]Website   link   bibtex  
Summary of the Survey of Field/Marine Station Directors and Managers. Doak, Thomas G.; Stewart, Craig A.; Wernert, Julie; Hancock, David Y.; Miller, T. Technical Report 7 2017.
Summary of the Survey of Field/Marine Station Directors and Managers [pdf]Paper   Summary of the Survey of Field/Marine Station Directors and Managers [link]Website   link   bibtex  
  2016 (70)
Jetstream – performance, early experiences, and early results. Stewart, C., A.; Hancock, D., Y.; Vaughn, M.; Fischer, J.; Cockerill, T.; Liming, L.; Merchant, N.; Miller, T.; Lowe, John Michael Stanzione, D., C.; Taylor, J.; and Skidmore, E. In Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, volume 17-21-July, pages 1-8, 2016. ACM Press
Jetstream – performance, early experiences, and early results [link]Website   doi   link   bibtex   abstract  
Big data, simulations and HPC convergence. Fox, G., C.; Qiu, J.; Jha, S.; Ekanayake, S.; and Kamburugamuve, S. Volume 10044 2016.
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Model-centric computation abstractions in machine learning applications. Zhang, B.; Peng, B.; and Qiu, J. In Proceedings of the 3rd ACM SIGMOD Workshop on Algorithms and Systems for MapReduce and Beyond, pages 3, 2016. ACM
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Software Frameworks for Deep Learning at Scale. Fox, J.; Zou, Y.; and Qiu, J. Technical Report 2016.
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Scalable Query and Analysis for Social Networks: An Integrated High-Level Dataflow System with Pig and Harp. Wu, T., S.; Zhang, B.; Clayton Davis, E.; Ferrara, A., F.; Menczer, F.; and Qiu, J. Big Data in Complex and Social Networks, pages 37-62. CRC Press, 2016.
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Facilitating Visualization Capacity Building. Byrd, V., L.; and Cottam, J., A. In Proceedings of the 9th International Symposium on Visual Information Communication and Interaction, pages 156, 2016. ACM
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Epoch Persistence: Safe, efficient, on-demand rendering for streaming data. Cottam, J., A.; and Lumsdaine, A. In System Sciences (HICSS), 2016 49th Hawaii International Conference on, pages 1730-1739, 2016. IEEE
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The Web's PKI: An Expository Review and Certificate Validation Cost Simulation. Heiland, R.; Garrison III, W., C.; Qiao, Y.; Lee, A., J.; and Welch, V. Technical Report 2016.
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High performance lda through collective model communication optimization. Zhang, B.; Peng, B., B.; and Qiu, J. Procedia Computer Science, 80: 86-97. 2016.
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Computational considerations in transcriptome assemblies and their evaluation, using high quality human RNA-Seq data. Ghaffari, N.; Abante, J.; Singh, R.; Blood, P., D.; and Johnson, C., D. In ACM International Conference Proceeding Series, volume 17-21-July, 2016. Association for Computing Machinery
Computational considerations in transcriptome assemblies and their evaluation, using high quality human RNA-Seq data [link]Website   doi   link   bibtex   abstract   1 download  
OSoMe: the IUNI observatory on social media. Davis, C., A.; Ciampaglia, G., L.; Aiello, L., M.; Chung, K.; Conover, M., D.; Ferrara, E.; Flammini, A.; Fox, G., C.; Gao, X.; and Gonçalves, B. PeerJ Computer Science, 2: e87. 2016.
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Genomic and metagenomic analysis of diversity-generating retroelements associated with Treponema denticola. Nimkulrat, S.; Lee, H.; Doak, T., G.; and Ye, Y. Frontiers in Microbiology, 7(JUN): pp 852. 2016.
Genomic and metagenomic analysis of diversity-generating retroelements associated with Treponema denticola [link]Website   doi   link   bibtex   abstract  
The advanced cyberinfrastructure research and education facilitators virtual residency: Toward a national cyberinfrastructure workforce. Neeman, H.; Ganote, C.; Kalescky, R.; Ramadugu, S., K.; Sherman, A., H.; Bergstrom, A.; Gray, Z.; Lemley, E.; Romanella, A.; Stengel, B.; Brunson, D.; Guilfoos, B.; Moore, B., G.; Rush, J.; and Voss, D. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (XSEDE16), volume 17-21-July, 7 2016. Association for Computing Machinery
The advanced cyberinfrastructure research and education facilitators virtual residency: Toward a national cyberinfrastructure workforce [pdf]Paper   doi   link   bibtex   abstract  
Disentangling the taxonomy of Rickettsiales and description of two novel symbionts ("Candidatus Bealeia paramacronuclearis" and "Candidatus Fokinia cryptica") sharing the cytoplasm of the ciliate protist Paramecium biaurelia. Szokoli, F.; Castelli, M.; Sabaneyeva, E.; Schrallhammer, M.; Krenek, S.; Doak, T., G.; Berendonk, T., U.; and Petroni, G. Applied and Environmental Microbiology, 82(24): 7236-7247. 2016.
Disentangling the taxonomy of Rickettsiales and description of two novel symbionts ("Candidatus Bealeia paramacronuclearis" and "Candidatus Fokinia cryptica") sharing the cytoplasm of the ciliate protist Paramecium biaurelia [link]Website   doi   link   bibtex   abstract  
The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway. Kucukyildirim, S.; Long, H.; Sung, W.; Miller, S., F.; Doak, T., G.; and Lynch, M. G3: Genes, Genomes, Genetics, 6(7): 2157-63. 2016.
The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway. [pdf]Paper   The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway. [link]Website   doi   link   bibtex   abstract  
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli. Lee, H.; Doak, T., G.; Popodi, E.; Foster, P., L.; and Tang, H. Nucleic Acids Research, 44(15): 7109-7119. 2016.
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli [link]Website   doi   link   bibtex   abstract  
System Acceptance Report for NSF award 1445604” High Performance Computing System Acquisition: Jetstream-A Self-Provisioned, Scalable Science and Engineering Cloud Environment”. Stewart, C., A.; Hancock, D., Y.; Vaughn, M.; Merchant, N., C.; Lowe, J., M.; Fischer, J.; Liming, L.; Taylor, J.; Afgan, E.; and Turner, G. Technical Report 2016.
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Jetstream (NSF Award 1445604) Year Program Year 2 Annual Report (Dec 1, 2015–Nov 30, 2016). Stewart, C., A.; Hancock, D., Y.; Vaughn, M.; Merchant, N.; Lowe, J., M.; Fischer, J.; Liming, L.; Taylor, J.; Afgan, E.; and Turner, G. Technical Report 2016.
Jetstream (NSF Award 1445604) Year Program Year 2 Annual Report (Dec 1, 2015–Nov 30, 2016) [link]Website   link   bibtex  
From describing to prescribing parallelism: Translating the SPEC ACCEL OpenACC suite to OpenMP target directives. Juckeland, G.; Hernandez, O.; Jacob, A., C.; Neilson, D.; Larrea, V., G., V.; Wienke, S.; Bobyr, A.; Brantley, W., C.; Chandrasekaran, S.; Colgrove, M.; Grund, A.; Henschel, R.; Joubert, W.; Müller, M., S.; Raddatz, D.; Shelepugin, P.; Whitney, B.; Wang, B.; and Kumaran, K. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 9945 LNCS: 470-488. 2016.
From describing to prescribing parallelism: Translating the SPEC ACCEL OpenACC suite to OpenMP target directives [link]Website   doi   link   bibtex   abstract  
Situating cyberinfrastructure in the public realm: The teragrid and XSEDE projects. Knepper, R.; and Chen, Y. In Kim Y., L., S., M., editor(s), ACM International Conference Proceeding Series, volume 08-10-June, pages 129-135, 2016. Association for Computing Machinery
Situating cyberinfrastructure in the public realm: The teragrid and XSEDE projects [link]Website   doi   link   bibtex   abstract  
High Performance Computing System Acquisition: Jetstream–A Self-Provisioned, Scalable Science and Engineering Cloud Environment (Year 1 Annual Report). Stewart, C., A.; Foster, I.; Merchant, N., C.; Taylor, J.; and Vaughn, M., W. Technical Report 2016.
High Performance Computing System Acquisition: Jetstream–A Self-Provisioned, Scalable Science and Engineering Cloud Environment (Year 1 Annual Report) [link]Website   link   bibtex  
Improving the scalability of a charge detection mass spectrometry workflow. McClary, S.; Henschel, R.; Thota, A.; Brunst, H.; and Draper, B. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (XSEDE16), volume 17-21-July, pages 8, 2016. Association for Computing Machinery
Improving the scalability of a charge detection mass spectrometry workflow [link]Website   doi   link   bibtex   abstract  
Jetstream–A Self-Provisioned, Scalable Science and Engineering Cloud Environment-NSF Acceptance Report. Stewart, C., A.; Foster, I.; Merchant, N., C.; Taylor, J.; and Vaughn, M., W. Technical Report 2016.
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Updated Acceptance Test Results for the Jetstream Production Environment. Hancock, D., Y.; Packard, M.; Turner, G.; and Stewart, C., A. Technical Report 2016.
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Comparing the consumption of CPU hours with scientific output for the extreme science and engineering discovery environment (XSEDE). Knepper, R.; and Börner, K. PLoS ONE, 11(6). 2016.
Comparing the consumption of CPU hours with scientific output for the extreme science and engineering discovery environment (XSEDE) [link]Website   doi   link   bibtex   abstract  
Bongo: A BGP speaker built for defending against bad routes. Benton, K.; Camp, L.; and Swany, M. In Proceedings - IEEE Military Communications Conference MILCOM, 2016.
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Provenance as Essential Infrastructure for Data Lakes [Preprint, forthcoming in IPAW 2016]. Suriarachchi, I.; and Plale, B. Technical Report 2016.
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Network-managed virtual global address space for message-driven runtimes. Kulkarni, A.; Dalessandro, L.; Kissel, E.; Lumsdaine, A.; Sterling, T.; and Swany, M. In HPDC 2016 - Proceedings of the 25th ACM International Symposium on High-Performance Parallel and Distributed Computing, 2016.
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Filtering Source-Spoofed IP Traffic Using Feasible Path Reverse Path Forwarding with SDN. Benton, K.; Camp, L., J.; Kelley, T.; and Swany, M. International Journal of Computer and Communication Engineering, 5(6): 441. 2016.
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Provenance as essential infrastructure for Data Lakes. Suriarachchi, I.; and Plale, B. Volume 9672 2016.
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Argus: A Multi-tenancy NoSQL store with workload-aware resource reservation. Zeng, J.; and Plale, B. Parallel Computing, 58. 2016.
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Horme: Random access big data analytics. Ruan, G.; and Plale, B. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, 2016.
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Photon: Remote memory access middleware for high-performance runtime systems. Kissel, E.; and Swany, M. In Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016, 2016.
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KVLight: A Lightweight Key-Value Store for Distributed Access in Cloud. Zeng, J.; and Plale, B. In Proceedings - 2016 16th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2016, 2016.
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SamzaSQL: Scalable fast data management with streaming SQL. Pathirage, M.; Hyde, J.; Pan, Y.; and Plale, B. In Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016, 2016.
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User managed virtual clusters in comet. Wagner, R.; Papadopoulos, P.; Mishin, D.; Cooper, T.; Tatineti, M.; Von Laszewski, G.; Wang, F.; and Fox, G., C., G. In ACM International Conference Proceeding Series, volume 17-21-July, 2016.
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Providing Statistical Reliability Guarantee for Cloud Clusters. Yang, Z.; Du, A., Y.; Das, S.; Ramesh, R.; Furlani, T.; von Laszewski, G.; and Qiao, C. In Providing Statistical Reliability Guarantee for Cloud Clusters. Submitted to Global Communications Conference, 2016.
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A multi-tenant fair share approach to full-text search engine. Peng, Z.; and Plale, B. In Proceedings of the 7th International Workshop on Data-Intensive Computing in the Cloud, pages 45-50, 2016. IEEE Press
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Big Data at Scale for Digital Humanities: An Architecture for the. Kowalczyk, S., T.; Sun, Y.; Peng, Z.; Plale, B.; Willis, C.; Zeng, J.; Pathirage, M.; Liyanage, S.; Todd, A.; and Ruan, G. Big Data: Concepts, Methodologies, Tools, and Applications: Concepts, Methodologies, Tools, and Applications,345. 2016.
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Analysis of memory constrained live provenance. Chen, P.; Evans, T.; and Plale, B. Volume 9672 2016.
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Offloading collective operations to programmable logic on a Zynq cluster. Arap, O.; and Swany, M. In Proceedings - 2016 IEEE 24th Annual Symposium on High-Performance Interconnects, HOTI 2016, 2016.
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Evaluating Collectives in Networks of Multicore/Two-level Reduction. Wickramasinghe, U., S.; D’Alessandro, L.; Lumsdaine, A.; Kissel, E.; Swany, M.; and Newton, R. 2016.
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Rapid Monitoring of Drought Impacts on Small-Scale Farms in Africa through Integration of Farmer SMS data and Environmental Sensors. Evans, T., P.; Caylor, K., K.; Estes, L., D.; Plale, B., A.; Attari, S.; and Waldman, K. In AGU Fall Meeting Abstracts, 2016.
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NIST Big Data Interoperability Framework: Volume 3, Use Cases and General Requirements (NIST Special Publication 1500-3). Subgroup, N., B., D., P., W., G., U., C., a., R. , 3(June). 2016.
NIST Big Data Interoperability Framework: Volume 3, Use Cases and General Requirements (NIST Special Publication 1500-3) [pdf]Website   doi   link   bibtex   abstract  
Crossing analytics systems: A case for integrated provenance in data lakes. Suriarachchi, I.; and Plale, B., A. In Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, pages 349-354, 10 2016. IEEE
Crossing analytics systems: A case for integrated provenance in data lakes [link]Website   doi   link   bibtex   abstract  
Anatomy of the SEAGrid Science Gateway. Nakandala, S.; Pamidighantam, S.; Yodage, S.; Doshi, N.; Abeysinghe, E.; Kankanamalage, C., P.; Marru, S.; and Pierce, M. In Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, pages 40, 2016. ACM Press
Anatomy of the SEAGrid Science Gateway [link]Website   doi   link   bibtex   abstract  
Integrating Apache Airavata with Docker, Marathon, and Mesos. Saha, P.; Govindaraju, M.; Marru, S.; and Pierce, M. Concurrency and Computation: Practice and Experience, 28(7): 1952-1959. 2016.
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GeoGateway: A system for analysis of UAVSAR data products. Donnellan, A.; Parker, J.; Glasscoe, M.; Granat, R.; Pierce, M.; Wang, J.; Ma, Y.; Ludwig, L., G.; and Rundle, J. In Geoscience and Remote Sensing Symposium (IGARSS), 2016 IEEE International, pages 210-213, 2016.
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Apache Airavata security manager: Authentication and authorization implementations for a multi-tenant escience framework. Nakandala, S.; Gunasinghe, H.; Marru, S.; and Pierce, M. In e-Science (e-Science), 2016 IEEE 12th International Conference on, pages 287-292, 2016.
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Community Science Exemplars in SEAGrid Science Gateway: Apache Airavata Based Implementation of Advanced Infrastructure. Pamidighantam, S.; Nakandala, S.; Abeysinghe, E.; Wimalasena, C.; Yodage, S., R.; Marru, S.; and Pierce, M. Procedia Computer Science, 80(C): 1927-1939. 2016.
Community Science Exemplars in SEAGrid Science Gateway: Apache Airavata Based Implementation of Advanced Infrastructure [link]Website   doi   link   bibtex   abstract  
GSoC 2015 student contributions to GenApp and Airavata. Brookes, E., H.; Kapoor, A.; Patra, P.; Marru, S.; Singh, R.; and Pierce, M. Concurrency and Computation: Practice and Experience, 28(7): 1960-1970. 2016.
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The Report of the 2016 Cybersecurity Summit for Large Facilities and Cyberinfrastructure: Strengthening Trustworthy Science. Marsteller, J.; Welch, V.; and Starzynski Coddens, A. Technical Report 2016.
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A Time of Turmoil. Cate, F., H.; Kuner, C.; Svantesson, D., J., B.; Lynsky, O.; and Millard, C. International Data Privacy Law, 6(1): 1-3. 2016.
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The Language of Data Privacy Law (and How It Differs from Reality). Cate, F., H.; Kuner, C.; Svantesson, D., J., B.; Lynskey, O.; and Millard, C. International Data Privacy Law, 4(1): 259-269. 2016.
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Modeling the Past and Future of Identity Management for Scientific Collaborations. Cowles, R.; Jackson, C.; and Welch, V. In Proceedings of the International Symposium on Grids and Clouds (ISGC) 2016. 13-18 March 2016. Academia Sinica, Taipei, Taiwan. Online at http://pos. sissa. it/cgi-bin/reader/conf. cgi? confid= 270, id. 14, 2016.
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The Global Data Protection Implications of" Brexit". Cate, F., H.; Kuner, C.; Svantesson, D., J., B.; Lynskey, O.; and Millard, C. International Data Privacy Law, 6(3): 167-169. 2016.
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PKI-ASAF Design Documents. Welch, V.; Heiland, R.; Garrison III, W., C.; and Lee, A., J. Technical Report 2016.
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Center for Trustworthy Scientific Cyberinfrastructure-The NSF Cybersecurity Center of Excellence: Year One Report. Welch, V. Technical Report 2016.
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The Medical Science DMZ. Peisert, S.; Barnett, W.; Dart, E.; Cuff, J.; Grossman, R., L.; Balas, E.; Berman, A.; Shankar, A.; and Tierney, B. Journal of the American Medical Informatics Association, 23(6): 1199-1201. 2016.
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SciGaP-CTSC Engagement Summary. Heiland, R.; Koranda, S.; and Welch, V. Technical Report 2016.
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Implementation of Simple XSEDE-Like Clusters: Science Enabled and Lessons Learned. Coulter, E.; Fischer, J.; Hallock, B.; Knepper, R.; and Stewart, C. In Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, volume 17-21-July, pages 1-8, 2016. ACM Press
Implementation of Simple XSEDE-Like Clusters: Science Enabled and Lessons Learned [link]Website   doi   link   bibtex   abstract  
Evaluation of SMP shared memory machines for use with in-memory and OpenMP big data applications. Younge, A., J.; Reidy, C.; Henschel, R.; and Fox, G., C. In Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016, pages 1597-1606, 2016. Institute of Electrical and Electronics Engineers Inc.
Evaluation of SMP shared memory machines for use with in-memory and OpenMP big data applications [link]Website   doi   link   bibtex   abstract  
NSF High Performance Computing System Acquisition system description: Jetstream-a self-provisioned, scalable science and engineering cloud environment. Stewart, C., A.; Stanzione, D.; Cockerill, T.; Skidmore, E.; Fischer, J.; Lowe, J., M.; Hammond, B.; Turner, G.; Hancock, D., Y.; and Miller, T. Technical Report 2016.
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Trident: Scalable compute archives: Workflows, visualization, and analysis. Gopu, A.; Hayashi, S.; Young, M., D.; Kotulla, R.; Henschel, R.; and Harbeck, D. Technical Report 2016.
Trident: Scalable compute archives: Workflows, visualization, and analysis [link]Website   doi   link   bibtex   abstract  
RabbitQR: Fast and flexible Big Data Processing at LSST data rates using existing, shared-use hardware. Kotulla, R.; Gopu, A.; and Hayashi, S. In SPIE 9913, Software and Cyberinfrastructure for Astronomy, 2016.
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Cyberinfrastructure as a Platform to Facilitate Effective Collaboration between Institutions and Support Collaboratories. Coulter, E.; Fischer, J.; Hallock, B.; Knepper, R.; Lifka, D.; Navarro, J.; Pierce, M.; and Stewart, C. In Proceedings of the 2016 ACM SIGUCCS Annual Conference, volume 06-09-Nove, pages 37-42, 11 2016. ACM
Cyberinfrastructure as a Platform to Facilitate Effective Collaboration between Institutions and Support Collaboratories [link]Website   doi   link   bibtex   abstract  
Gathering requirements for advancing simulations in HPC infrastructures via science gateways. Gesing, S.; Dooley, R.; Pierce, M.; Krüger, J.; Grunzke, R.; Herres-Pawlis, S.; and Hoffmann, A. Future Generation Computer Systems, 82: 544-554. 5 2016.
Gathering requirements for advancing simulations in HPC infrastructures via science gateways [link]Website   doi   link   bibtex   abstract  
  2015 (97)
Jetstream: a self-provisioned, scalable science and engineering cloud environment. Stewart, C., A.; Cockerill, T., M.; Foster, I.; Hancock, D.; Merchant, N.; Skidmore, E.; Stanzione, D.; Taylor, J.; Tuecke, S.; Turner, G.; Vaughn, M.; and Gaffney, N., I. In Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, volume 2015-July, pages 1-8, 2015. ACM Press
Jetstream: a self-provisioned, scalable science and engineering cloud environment [link]Website   doi   link   bibtex   abstract  
Dynamic parallelism for simple and efficient gpu graph algorithms. Zhang, P.; Holk, E.; Matty, J.; Misurda, S.; Zalewski, M.; Chu, J.; McMillan, S.; and Lumsdaine, A. In Proceedings of the 5th Workshop on Irregular Applications: Architectures and Algorithms, pages 11, 2015. ACM
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Dynamic Adaptation for Elastic System Services Using Virtual Servers. Kulkarni, A.; Greenberg, H.; Lang, M.; and Lumsdaine, A. In High Performance Computing (HiPC), 2015 IEEE 22nd International Conference on, pages 125-134, 2015. IEEE
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Fast Data Management with Distributed Streaming SQL. Pathirage, M.; and Plale, B. arXiv preprint arXiv:1511.03935. 2015.
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Towards an Understanding of Scalable Query and Data Analysis for Social Media Data using High-Level Dataflow Systems. Wu, T., L., S.; and Qiu, J. In SC15 27th annual International Conference for High Performance Computing, Networking, Storage and Analysis, 2015.
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Parallel LDA through synchronized communication optimizations. Zhang, B.; Peng, B.; and Qiu, J. Technical Report 2015.
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Towards a comprehensive set of big data benchmarks. Fox, G., C.; Jha, S.; Qiu, J.; Ekanazake, S.; and Luckow, A. Big Data and High Performance Computing, 26: 47. 2015.
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Parallel clustering of high-dimensional social media data streams. Gao, X.; Ferrara, E.; and Qiu, J. In Cluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposium on, pages 323-332, 2015. IEEE
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A High Order Multi-Scale Numerical Approach for Kinetic Simulations. Qiu, J. Technical Report 2015.
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Cyberinfrastructure Value Assessment Report. DeStafano, L., L., R. Technical Report I-STEM Education Initiative University of Illinois at Urbana-Champaign, 2015.
Cyberinfrastructure Value Assessment Report [link]Website   link   bibtex  
Scalable Relativistic High-Resolution Shock-Capturing for Heterogeneous Computing. Glines, F., W.; Anderson, M.; and Neilsen, D. In Cluster Computing (CLUSTER), 2015 IEEE International Conference on, pages 611-618, 2015. IEEE
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Relativistic Hydrodynamics with Wavelets. DeBuhr, J.; Zhang, B.; Anderson, M.; Neilsen, D.; and Hirschmann, E., W. arXiv preprint arXiv:1512.00386. 2015.
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Pixel-oriented techniques for visualizing next-generation HPC systems. Cottam, J.; Martin, B.; Dalessandro, L.; and Lumsdaine, A. In Software Visualization (VISSOFT), 2015 IEEE 3rd Working Conference on, pages 160-164, 2015. IEEE
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Supervised classification of enzyme residue function using machine learning methods. Youn, E.; Radivojac, P.; Peters, B.; Moad, C.; Heiland, R.; and Mooney, S., D. Machine Learning and Applications: An International Journa, 2. 2015.
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White Paper: Big Data, Simulations and HPC Convergence. Fox, G., C.; Qiu, J.; Jha, S.; Ekanayake, S.; and Kamburugamuve, S. In Workshop on Big Data Benchmarks, volume 16, pages 3-17, 2015. Springer
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Harp: Collective communication on hadoop. Zhang, B.; Ruan, Y.; and Qiu, J. In Cloud Engineering (IC2E), 2015 IEEE International Conference on, pages 228-233, 2015. IEEE
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Hpc-abds high performance computing enhanced apache big data stack. Fox, G., G., C.; Qiu, J.; Kamburugamuve, S.; Jha, S.; and Luckow, A. In Cluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposium on, pages 1057-1066, 2015. IEEE
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Importance of runtime considerations in performance engineering of large-scale distributed graph algorithms. Firoz, J., S.; Kanewala, T., A.; Zalewski, M.; Barnas, M.; and Lumsdaine, A. In European Conference on Parallel Processing, pages 553-564, 2015. Springer
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Comparison of single source shortest path algorithms on two recent asynchronous many-task runtime systems. Firoz, J., S.; Barnas, M.; Zalewski, M.; and Lumsdaine, A. In Parallel and Distributed Systems (ICPADS), 2015 IEEE 21st International Conference on, pages 674-681, 2015. IEEE
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Sustained software for cyberinfrastructure: Analyses of successful efforts with a focus on NSF-funded software. Stewart, C., A.; Barnett, W., K.; Wernert, E., A.; Wernert, J., A.; Welch, V.; and Knepper, R. In Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15, pages 63-72, 2015. ACM Press
Sustained software for cyberinfrastructure: Analyses of successful efforts with a focus on NSF-funded software [link]Website   doi   link   bibtex   abstract  
Apache Airavata as a Laboratory - Architecture and Case Study for Component-Based Gateway Middleware. Marru, S.; Pierce, M.; Pamidighantam, S.; and Wimalasena, C. In Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15, pages 19-26, 2015. ACM Press
Apache Airavata as a Laboratory - Architecture and Case Study for Component-Based Gateway Middleware [link]Website   doi   link   bibtex   abstract  
Potential for a large earthquake near Los Angeles inferred from the 2014 La Habra earthquake. Donnellan, A.; Grant Ludwig, L.; Parker, J., W.; Rundle, J., B.; Wang, J.; Pierce, M.; Blewitt, G.; and Hensley, S. Earth and Space Science, 2(9): 378-385. 2015.
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Web Services for Dynamic Coloring of UAVSAR Images. Wang, J.; Pierce, M.; Donnellan, A.; and Parker, J. Pure and Applied Geophysics, 172(8): 2325-2332. 2015.
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Science gateways-leveraging modeling and simulations in HPC infrastructures via increased usability. Gesing, S.; Dooley, R.; Pierce, M.; Krüger, J.; Grunzke, R.; Herres-Pawlis, S.; and Hoffmann, A. In High Performance Computing & Simulation (HPCS), 2015 International Conference on, pages 19-26, 2015.
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The GenApp framework integrated with Airavata for managed compute resource submissions. Brookes, E., H.; Anjum, N.; Curtis, J., E.; Marru, S.; Singh, R.; and Pierce, M. Concurrency and Computation: Practice and Experience, 27(16): 4292-4303. 2015.
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Multihazard simulation and cyberinfrastructure. Donnellan, A.; Williams, C.; and Pierce, M. Pure and Applied Geophysics, 172(8): 2083-2085. 2015.
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Publishing and consuming GLUE v2.0 resource information in XSEDE. Smith, W.; Pamidighantam, S.; and Navarro, J. In Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, volume 2015-July, pages 1-8, 7 2015. ACM Press
Publishing and consuming GLUE v2.0 resource information in XSEDE [pdf]Paper   Publishing and consuming GLUE v2.0 resource information in XSEDE [link]Website   doi   link   bibtex   abstract  
Ab Initio Studies of Calcium Carbonate Hydration. Lopez-Berganza, J., A.; Diao, Y.; Pamidighantam, S.; and Espinosa-Marzal, R., M. The Journal of Physical Chemistry A, 119(47): 11591-11600. 11 2015.
Ab Initio Studies of Calcium Carbonate Hydration [pdf]Paper   Ab Initio Studies of Calcium Carbonate Hydration [link]Website   doi   link   bibtex   abstract  
XSEDE value added, cost avoidance, and return on investment. Stewart, C., A.; Roskies, R.; Knepper, R.; Moore, R., L.; Whitt, J.; and Cockerill, T., M. In Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, volume 2015-July, pages 1-8, 7 2015. ACM Press
XSEDE value added, cost avoidance, and return on investment [pdf]Paper   XSEDE value added, cost avoidance, and return on investment [link]Website   doi   link   bibtex   abstract  
Saccharide breakdown and fermentation by the honey bee gut microbiome. Lee, F., J.; Rusch, D., B.; Stewart, F., J.; Mattila, H., R.; and Newton, I., L. Environmental Microbiology, 17(3): 796-815. 3 2015.
Saccharide breakdown and fermentation by the honey bee gut microbiome [pdf]Paper   doi   link   bibtex   abstract  
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. Wang, M.; Doak, T., G.; and Ye, Y. Genome Biology, 16(1). 2015.
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes [link]Website   doi   link   bibtex   abstract  
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Bao, G.; Wang, M.; Doak, T., G.; and Ye, Y. Frontiers in Microbiology, 6(SEP). 2015.
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota [link]Website   doi   link   bibtex   abstract  
Draft genome sequence of Caedibacter varicaedens, a kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia. Suzuki, H.; Dapper, A., L.; Jackson, C., E.; Lee, H.; Pejaver, V.; Doak, T., G.; Lynch, M.; and Preer J.R., J. Genome Announcements, 3(6). 2015.
Draft genome sequence of Caedibacter varicaedens, a kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia [link]Website   doi   link   bibtex   abstract  
Mutation rate, spectrum, topology and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens Migula ATCC948. Long, H.; Sung, W.; Miller, S., F.; Ackerman, M., S.; Doak, T., G.; and Lynch, M. GENOME BIOLOGY AND EVOLUTION, 23: 262-271. 2015.
Mutation rate, spectrum, topology and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens Migula ATCC948 [link]Website   link   bibtex  
Background mutational features of the radiation-resistant bacterium deinococcus radiodurans. Long, H.; Kucukyildirim, S.; Sung, W.; Williams, E.; Lee, H.; Ackerman, M., S.; Doak, T., G.; Tang, H.; and Lynch, M. Molecular Biology and Evolution, 32(9): 2383-2392. 2015.
Background mutational features of the radiation-resistant bacterium deinococcus radiodurans [link]Website   doi   link   bibtex   abstract  
The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Farlow, A.; Long, H.; Arnoux, S.; Sung, W.; Doak, T., G.; Nordborg, M.; and Lynch, M. Genetics, 201(2): 737-744. 2015.
The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe [link]Website   doi   link   bibtex   abstract  
Describing and predicting developmental profiles of externalizing problems from childhood to adulthood. Petersen, I., T.; Bates, J., E.; Dodge, K., A.; Lansford, J., E.; and Pettit, G., S. DEVELOPMENT AND PSYCHOPATHOLOGY. 2015.
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NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture. Seetharam, A.; Gomez, A.; Purcell, C., M.; Hyde, J., R.; Blood, P., D.; and Severin, A., J. In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure (XSEDE '15), pages 5, 2015.
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Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome. Wu, L.; Ganote, C., L.; Doak, T., G.; Barnett, W.; Mockaitis, K.; and Stewart, C., A. In Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, volume 2015-July, pages 1-6, 7 2015. ACM Press
Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome [link]Website   doi   link   bibtex   abstract  
Research proposal: Barriers to new user and new domain adoption of the XSEDE cyberinfrastructure. Knepper, R. In Paprzycki M. Maciaszek L., G., M., M., L., editor(s), Proceedings of the 2015 Federated Conference on Computer Science and Information Systems, FedCSIS 2015, pages 1023-1028, 2015. Institute of Electrical and Electronics Engineers Inc.
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Performance Optimization for the Trinity RNA-Seq Assembler. Wagner, M.; Fulton, B.; and Henschel, R. Tools for High Performance Computing. 2015.
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Scalability testing of dne2 in lustre 2.7. Crowe, T.; Lavender, N.; and Simms, S. Lustre Users Group. 2015.
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UITS Research Technologies update. Stewart, C., A. Technical Report 2015.
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Workshop Report: Campus Bridging: Reducing Obstacles on the Path to Big Answers 2015. Hallock, B.; Knepper, R.; and Stewart, C., A. Technical Report Indiana University, 9 2015.
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Facilitating scientific collaborations by delegating identity management: Reducing barriers & roadmap for incremental implementation. Cowles, R.; Jackson, C.; and Welch, V. In CLHS 2015 - Proceedings of the 2015 Workshop on Changing Landscapes in HPC Security, Part of HPDC 2015, pages 15-19, 2015. Association for Computing Machinery, Inc
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Provenance and Annotation of Data and Processes: 5th International Provenance and Annotation Workshop, IPAW 2014, Cologne, Germany, June 9-13, 2014. Revised Selected Papers. Ludäscher, B.; and Plale, B. Volume 8628 Springer, 2015.
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Big data provenance analysis and visualization. Chen, P.; and Plale, B. In Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015, 2015.
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Regenerating and quantifying quality of benchmarking data using static and dynamic provenance. Ghoshal, D.; Chauhan, A.; and Plale, B. Volume 8628 2015.
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Using phoebus data transfer accelerator in cloud environments. Zhang, M.; Kissel, E.; and Swany, M. In IEEE International Conference on Communications, volume 2015-Septe, 2015.
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Workload-aware resource reservation for multi-tenant NoSQL. Zeng, J.; and Plale, B. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, volume 2015-Octob, 2015.
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Parallel and quantitative sequential pattern mining for large-scale interval-based temporal data. Ruan, G.; Zhang, H.; and Plale, B. In Proceedings - 2014 IEEE International Conference on Big Data, IEEE Big Data 2014, 2015.
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Adaptive Recursive Doubling Algorithm for Collective Communication. Arap, O.; Swany, M.; Brown, G.; and Himebaugh, B. In Proceedings - 2015 IEEE 29th International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2015, 2015.
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Towards building a lightweight key-value store on parallel file system. Zeng, J.; and Plale, B. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, volume 2015-Octob, 2015.
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Filtering IP source spoofing using feasible path reverse path forwarding with SDN. Benton, K.; Camp, L.; Kelley, T.; and Swany, M. In 2015 IEEE Conference on Communications and NetworkSecurity, CNS 2015, 2015.
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Preface. Ludäscher, B.; and Plale, B. Volume 8628 2015.
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HELM: Conflict-free active measurement scheduling for shared network resource management. Zhang, M.; Swany, M.; Yavanamanda, A.; and Kissel, E. In Proceedings of the 2015 IFIP/IEEE International Symposium on Integrated Network Management, IM 2015, 2015.
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Trust threads: minimal provenance and data publication and reuse. Plale, B. In National Data Integrity Conference-2015, 2015. Colorado State University. Libraries
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New Approaches to Capture High Frequency Agricultural Dynamics in Africa through Mobile Phones. Evans, T., P.; Attari, S.; Plale, B., A.; Caylor, K., K.; Estes, L., D.; and Sheffield, J. In AGU Fall Meeting Abstracts, 2015.
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NIST Special Publication 1500-6 : NIST Big Data Interoperability Framework - Reference Architecture. (NBD-PWG), N., B., D., P., W., G. , 6(June): 1-62. 2015.
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Peer comparison of XSEDE and NCAR publication data. Von Laszewski, G.; Wang, F.; Fox, G., C., G.; Hart, D.; Furlani, T.; Deleon, R.; and Gallo, S. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, volume 2015-Octob, 2015.
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Scalability Analysis of the Multi-Look Time Domain Processor on XSEDE Compute Resources. von Laszewski, G.; Wang, F.; Fox, G., C.; Li, J.; and Paden, J. Technical Report 2015.
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Physiological effects of heat stress on Hawaiian picture-wing Drosophila: Genome-wide expression patterns and stress-related traits. Uy, K., L.; LeDuc, R.; Ganote, C.; and Price, D., K. Conservation Physiology, 3(1). 2015.
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TAS view of XSEDE users and usage. DeLeon, R.; Furlani, T.; Gallo, S.; White, J.; Jones, M.; Patra, A.; Innus, M.; Yearke, T.; Palmer, J.; Sperhac, J.; Rathsam, R.; Simakov, N.; Von Laszewski, G.; and Wang, F. In ACM International Conference Proceeding Series, volume 2015-July, 2015.
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Towards sustainable curation and preservation: The SEAD project's data services approach. Myers, J.; Hedstrom, M.; Akmon, D.; Payette, S.; Plale, B.; Kouper, I.; McCaulay, S.; McDonald, R.; Suriarachchi, I.; Varadharaju, A.; Kumar, P.; Elag, M.; Lee, J.; Kooper, R.; and Marini, L. In Proceedings - 11th IEEE International Conference on eScience, eScience 2015, 2015.
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Komadu: A capture and visualization system for scientific data provenance. Suriarachchi, I.; Zhou, Q.; and Plale, B. Journal of Open Research Software, 3(1). 2015.
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Research challenges in future multi-domain network performance measurement and monitoring. Calyam, P.; and Swany, M. Computer Communication Review, 45(3). 2015.
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ProvErr: System level statistical fault diagnosis using dependency model. Chen, P.; and Plale, B. In Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015, 2015.
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Software in Science: a Report of Outcomes of the 2014 National Science Foundation Software Infrastructure for Sustained Innovation (SI2) Meeting. Plale, B.; Jones, M.; and Thain, D. Technical Report 2015.
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The Data Capsule for Non-Consumptive Research. Plale, B.; Prakash, A.; and McDonald, R. Technical Report 2015.
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Advantages to Geoscience and disaster response from QuakeSim implementation of interferometric radar maps in a GIS database system. Parker, J.; Donnellan, A.; Glasscoe, M.; Fox, G., C.; Wang, J.; Pierce, M.; Ma, Y.; Wang, J.; and Ma, Y. Pure and Applied Geophysics, 172(8): 2295-2304. 2015.
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Disaster Response Tools for Decision Support and Data Discovery-E-DECIDER and GeoGateway. Glasscoe, M., T.; Donnellan, A.; Parker, J., W.; Granat, R., A.; Lyzenga, G., A.; Pierce, M., E.; Wang, J.; Grant Ludwig, L.; Eguchi, R., T.; Huyck, C., K.; and others In AGU Fall Meeting Abstracts, 2015.
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An Overview of the XSEDE Extended Collaborative Support Program. Wilkins-Diehr, N.; Sanielevici, S.; Alameda, J.; Cazes, J.; Crosby, L.; Pierce, M.; and Roskies, R. In Gitler I., K., J., editor(s), International Conference on Supercomputing, volume 595, pages 3-13, 2015. Springer Verlag
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E-decider: Using earth science data and modeling tools to develop decision support for earthquake disaster response. Glasscoe, M., T.; Wang, J.; Pierce, M., E.; Yoder, M., R.; Parker, J., W.; Burl, M., C.; Stough, T., M.; Granat, R., A.; Donnellan, A.; Rundle, J., B.; and others Pure and Applied Geophysics, 172(8): 2305-2324. 2015.
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XSIM Final Report: Modelling the Past and Future of Identity Management for Scientific Collaborations. Cowles, R.; Jackson, C.; and Welch, V. Technical Report Indiana University, 9 2015.
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Risk Management in Data Protection. Cate, F., H.; Kuner, C.; Millard, C.; Svantesson, D., J., B.; and Lynskey, O. International Data Privacy Law, 5(2): 95-98. 2015.
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Center for Applied Cybersecurity Research: 2015 Annual Report and Strategic Plan (2015-2020). Delaney, D., G.; Welch, V.; and Starzynski Coddens, A. Technical Report 2015.
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Facilitating Scientific Collaborations by Delegating Identity Management. Cowles, R.; Jackson, C.; and Welch, V. In Proceedings of the 2015 Workshop on Changing Landscapes in HPC Security - CLHS '15, pages 15-19, 2015. ACM Press
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Protecting Privacy in Big Data. Cate, F., H. Journal of Law and Economic Regulation, 8(1): 7-20. 2015.
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The Data Protection Credibility Crisis. Cate, F., H.; Kuner, C.; Millard, C.; Svantesson, D., J., B.; and Lynskey, O. International Data Privacy Law, 5: 3. 2015.
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Internet Balkanization Gathers Pace: Is Privacy the Real Driver?. Cate, F., H.; Kuner, C.; Millard, C.; Svantesson, D., J., B.; and Lynskey, O. International Data Privacy Law, 5(1): 1-2. 2015.
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Apache Airavata: design and directions of a science gateway framework. Pierce, M., E.; Marru, S.; Gunathilake, L.; Wijeratne, D., K.; Singh, R.; Wimalasena, C.; Ratnayaka, S.; and Pamidighantam, S. Concurrency and Computation: Practice and Experience, 27(16): 4282-4291. 11 2015.
Apache Airavata: design and directions of a science gateway framework [link]Website   doi   link   bibtex   abstract  
Programmable Immersive Peripheral Environmental System (PIPES): A prototype control system for environmental feedback devices. Frend, C.; and Boyles, M. In Dolinsky M., M., I., E., editor(s), Proceedings of SPIE - The International Society for Optical Engineering, volume 9392, 2015. SPIE
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SPEC ACCEL: A standard application suite for measuring hardware accelerator performance. Juckeland, G.; Brantley, W.; Chandrasekaran, S.; Chapman, B.; Che, S.; Colgrove, M.; Feng, H.; Grund, A.; Henschel, R.; Hwu, W.; Li, H.; Müller, M., S.; Nagel, W., E.; Perminov, M.; Shelepugin, P.; Skadron, K.; Stratton, J.; Titov, A.; Wang, K.; Van Waveren, M.; Whitney, B.; Wienke, S.; Xu, R.; and Kumaran, K. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8966: 46-67. 2015.
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Cyberinfrastructure Begins at Home. Hancock, D., Y.; Henschel, R.; Kallback-Rose, K.; and Stewart, C., A. In SPXXL Winter Workshop, 2015.
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IU PTI/UITS Research Technologies Annual Report: FY 2014. Stewart, C., A.; and Miller, T. Technical Report 2015.
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Authentication and Authorization Considerations for a Multi-tenant Service. Heiland, R.; Koranda, S.; Marru, S.; Pierce, M.; and Welch, V. In Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15, pages 29-35, 2015. ACM Press
Authentication and Authorization Considerations for a Multi-tenant Service [link]Website   doi   link   bibtex   abstract  
Science gateways today and tomorrow: Positive perspectives of nearly 5000 members of the research community. Lawrence, K., A.; Zentner, M.; Wilkins-Diehr, N.; Wernert, J., A.; Pierce, M.; Marru, S.; and Michael, S. Concurrency Computation , 27(16): 4252-4268. 2015.
Science gateways today and tomorrow: Positive perspectives of nearly 5000 members of the research community [link]Website   doi   link   bibtex   abstract  
XCBC and XNIT - Tools for Cluster Implementation and Management in Research and Training. Fischer, J.; Coulter, E.; Knepper, R.; Peck, C.; and Stewart, C., A. In 2015 IEEE International Conference on Cluster Computing, volume 2015-Octob, pages 857-864, 9 2015. IEEE
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Building a Chemical-Protein Interactome on the Open Science Grid. Quick, R.; Hayashi, S.; Meroueh, S.; Rynge, M.; Teige, S.; Wang, B.; Xu, D.; Sinica, A.; and Taipei, T. In International Symposium on Grids and Clouds (ISGC), pages 15-20, 2015.
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Jetstream: A Distributed Cloud Infrastructure for Under Resourced Higher Education Communities. Fischer, J.; Tuecke, S.; Foster, I.; and Stewart, C., A. In Proceedings of the 1st Workshop on The Science of Cyberinfrastructure Research, Experience, Applications and Models - SCREAM '15, pages 53-61, 6 2015. ACM Press
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Enabling large scale next-generation sequence assembly with Blacklight. Couger, B., M.; Pipes, L.; Squina, F.; Prade, R.; Siepel, A.; Palermo, R.; Katze, M., G.; Mason, C., E.; and Blood, P., D. CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE. 2014.
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Distributed control: priority scheduling for single source shortest paths without synchronization. Zalewski, M.; Kanewala, T., A.; Firoz, J., S.; and Lumsdaine, A. In Proceedings of the 4th Workshop on Irregular Applications: Architectures and Algorithms, pages 17-24, 2014. IEEE Press
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Region-based memory management for GPU programming languages: enabling rich data structures on a spartan host. Holk, E.; Newton, R.; Siek, J.; and Lumsdaine, A. ACM SIGPLAN Notices, 49(10): 141-155. 2014.
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Towards Automated Coding of Program Comprehension Gaze Data. Hansen, M.; Goldstone, R., L.; and Lumsdaine, A. Eye Movements in Programming Education,9. 2014.
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Scoping Rules on a Platter. Voufo, L.; Zalewski, M.; and Lumsdaine, A. In Proceedings of the 10th ACM SIGPLAN workshop on Generic programming, pages 59-70, 2014.
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A dynamic execution model applied to distributed collision detection. Anderson, M.; Brodowicz, M.; Dalessandro, L.; DeBuhr, J.; and Sterling, T. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8488 LNCS: 470-477. 2014.
A dynamic execution model applied to distributed collision detection [link]Website   doi   link   bibtex   abstract  
Offloading MPI Parallel Prefix Scan (MPI_Scan) with the NetFPGA. Arap, O.; and Swany, M. arXiv preprint arXiv:1408.4939. 2014.
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Special issue for emerging computational methods for the life sciences workshop. Qiu, J.; Foster, I.; and Taylor, R. Concurrency Computation Practice and Experience, 26(4). 2014.
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Integrating pig with harp to support iterative applications with fast cache and customized communication. Wu, T.; Koppula, A.; and Qiu, J. In Proceedings of DataCloud 2014: 5th International Workshop on Data Intensive Computing in the Clouds - Held in Conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2014.
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Towards an understanding of facets and exemplars of big data applications. Fox, G., C.; Jha, S.; Qiu, J.; and Luckow, A. In Proceedings of the 20 Years of Beowulf Workshop on Honor of Thomas Sterling's 65th Birthday, pages 7-16, 2014. ACM
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Integrating Pig with Harp to support iterative applications with fast cache and customized communication. Wu, T.; Koppula, A.; and Qiu, J. In Proceedings of the 5th International Workshop on Data-Intensive Computing in the Clouds, pages 33-39, 2014. IEEE Press
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Integrating the Apache Big Data Stack with HPC for Big Data. Fox, G., C.; Qiu, J.; and Jha, S. In AGU Fall Meeting Abstracts, 2014.
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Cloud Computing for Data-Intensive Applications. Li, X.; and Qiu, J. Volume 1 Springer, 2014.
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Towards HPC-ABDS: an initial high-performance big data stack. Qiu, J.; Jha, S.; Luckow, A.; and Fox, G., C. Building Robust Big Data Ecosystem ISO/IEC JTC, 1: 18-21. 2014.
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Comparative study on structure and correlation among author co-occurrence networks in bibliometrics. Qiu, J.; Dong, K.; and Yu, H. Scientometrics, 101(2): 1345-1360. 2014.
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Supporting a social media observatory with customizable index structures: architecture and performance. Gao, X.; Roth, E.; McKelvey, K.; Davis, C.; Younge, A.; Ferrara, E.; Menczer, F.; and Qiu, J. Cloud Computing for Data-Intensive Applications, pages 401-427. Springer, 2014.
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Parallelizing Big Data Machine Learning Algorithms with Model Rotation. Zhang, B.; Peng, B.; and Qiu, J. NIPS. 2014.
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SLOWER: A performance model for Exascale computing. Sterling, T.; Kogler, D.; Anderson, M.; and Brodowicz, M. Supercomputing frontiers and innovations, 1(2): 42-57. 2014.
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Towards exascale co-design in a runtime system. Sterling, T.; Anderson, M.; Bohan, P., K.; Brodowicz, M.; Kulkarni, A.; and Zhang, B. In International Conference on Exascale Applications and Software, pages 85-99, 2014. Springer
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Abstract rendering: Out-of-core rendering for information visualization. Cottam, J., A.; Lumsdaine, A.; and Wang, P. In Visualization and Data Analysis 2014, volume 9017, pages 90170K, 2014. International Society for Optics and Photonics
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Preserving Data While Rendering. Cottam, J., A.; and Wang, P. Parsons Journal for Information Mapping, 6(1). 2014.
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The green bank northern celestial cap pulsar survey. I. Survey description, data analysis, and initial results. Stovall, K.; Lynch, R., S.; Ransom, S., M.; Archibald, A., M.; Banaszak, S.; Biwer, C., M.; Boyles, J.; Dartez, L., P.; Day, D.; and Ford, A., J. The Astrophysical Journal, 791(1): 67. 2014.
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Emerging Computational Methods for the Life Sciences Workshop 2012. Qiu, J.; Foster, I.; and Goble, C. Concurrency and Computation: Practice and Experience, 26(6): 1231-1233. 2014.
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A tale of two data-intensive paradigms: Applications, abstractions, and architectures. Jha, S.; Qiu, J.; Luckow, A.; Mantha, P.; and Fox, G., C., G. In Big Data (BigData Congress), 2014 IEEE International Congress on, pages 645-652, 2014. IEEE
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IceCube Cybersecurity Improvement Plan. Marsteller, J.; and Heiland, R. Technical Report 2014.
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The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Sluka, J., P.; Shirinifard, A.; Swat, M.; Cosmanescu, A.; Heiland, R., W.; and Glazier, J., A. Bioinformatics, 30(16): 2367-2374. 2014.
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PXFS: A persistent storage model for extreme scale. Yang, S.; Brodowicz, M.; Ligon III, W., B.; and Kaiser, H. In 2014 International Conference on Computing, Networking and Communications, ICNC 2014, pages 900-906, 2014. IEEE Computer Society
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Supporting queries and analyses of large-scale social media data with customizable and scalable indexing techniques over NoSQL databases. Gao, X.; and Qiu, J. In Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on, pages 587-590, 2014. IEEE
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Approaches to understanding the impact of technologies for aging in place: a mini-review. Connelly, K.; Mokhtari, M.; and Falk, T., H. Gerontology, 60(3): 282-288. 2014.
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Routing events using the Grid Event Service. Pallickara, S.; and Fox, G., C. Technical Report 2014.
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Search for invisible decays of a Higgs boson produced in association with a Z boson in ATLAS. Aad, G.; Abajyan, T.; Abbott, B.; Abdallah, J.; Khalek, S., A.; Abdinov, O.; Aben, R.; Abi, B.; Abolins, M.; and AbouZeid, O., S. Physical Review Letters, 112(20): 201802. 2014.
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Property Damage, Purchasing Orders, and Power Outages, Oh My!: Suggestions for Planning Your Next In-The-Wild Deployment. Hazlewood, W., R.; Connelly, K.; Caine, K., E.; Schall-Zimmerman, Z.; and Blanton, G. Handbook of Smart Homes, Health Care and Well-Being,1-14. 2014.
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Designing Aging-In-Place Technologies to Reflect the Lifestyles and Precious Artifacts of Urban and Rural Older Adults. White, G.; Evans, R.; Connelly, K.; and Caine, K. In Proceedings of the Human Factors and Ergonomics Society Annual Meeting, volume 58, pages 145-149, 2014. SAGE Publications Sage CA: Los Angeles, CA
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PM2: A Partitioning-Mining-Measuring Method for Identifying Progressive Changes in Older Adults’ Sleeping Activity. Lin, Q.; Zhang, D.; Connelly, K.; Zhou, X.; and Ni, H. Journal of healthcare engineering, 5(2): 205-228. 2014.
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Designing consumer health technologies for the treatment of patients with depression: A health practitioner's perspective. White, G.; Caine, K.; Connelly, K.; Selove, R.; and Doub, T. Interactive journal of medical research, 3(1). 2014.
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Privacy concerns in assisted living technologies. Garg, V.; Camp, L., J.; Lorenzen-Huber, L.; Shankar, K.; and Connelly, K. annals of telecommunications-annales des télécommunications, 69(1-2): 75-88. 2014.
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David J. Crandall. Ahmed, T.; Hoyle, R.; Shaffer, P.; and Connelly, K. Technical Report 2014.
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Scoping rules on a platter: A framework for understanding and specifying name binding. Voufo, L.; Zalewski, M.; and Lumsdaine, A. In Proceedings of the 10th ACM SIGPLAN workshop on Generic programming, pages 59-70, 2014. ACM
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Towards a collective layer in the big data stack. Gunarathne, T.; Qiu, J.; and Gannon, D. In Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on, pages 236-245, 2014. IEEE
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Integrating science gateways with xsede security: A survey of credential management approaches. Basney, J.; Gaynor, J.; Marru, S.; Pierce, M.; Kanewala, T., A.; Dooley, R.; and Stubbs, J. In Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, pages 58, 2014.
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The apache airavata application programming interface: Overview and evaluation with the Ultrascan Science Gateway. Pierce, M.; Marru, S.; Demeler, B.; Singh, R.; and Gorbet, G. In Proceedings of the 9th Gateway Computing Environments Workshop (GCE '14), pages 25-29, 2014. Institute of Electrical and Electronics Engineers Inc.
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E-DECIDER Disaster Response and Decision Support Cyberinfrastructure: Technology and Challenges. Glasscoe, M., T.; Parker, J., W.; Pierce, M., E.; Wang, J.; Eguchi, R., T.; Huyck, C., K.; Hu, Z.; Chen, Z.; Yoder, M., R.; Rundle, J., B.; and others In AGU Fall Meeting Abstracts, 2014.
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Combined UAVSAR and GPS Estimates of Fault Slip for the M 6.0 South Napa Earthquake. Donnellan, A.; Parker, J., W.; Hawkins, B.; Hensley, S.; Jones, C., E.; Owen, S., E.; Moore, A., W.; Wang, J.; Pierce, M., E.; and Rundle, J., B. In AGU Fall Meeting Abstracts, 2014.
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UAVSAR observations of triggered slip on the Imperial, Superstition Hills, and East Elmore Ranch Faults associated with the 2010 M 7.2 El Mayor-Cucapah earthquake. Donnellan, A.; Parker, J.; Hensley, S.; Pierce, M.; Wang, J.; and Rundle, J. Geochemistry, Geophysics, Geosystems, 15(3): 815-829. 2014.
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E-DECIDER Rapid Response to the M 6.0 South Napa Earthquake. Glasscoe, M., T.; Parker, J., W.; Pierce, M., E.; Wang, J.; Eguchi, R., T.; Huyck, C., K.; Hu, Z.; Chen, Z.; Yoder, M., R.; Rundle, J., B.; and others In AGU Fall Meeting Abstracts, 2014.
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CTSC Recommended Security Practices for Thrift Clients: Case Study-Evernote. Heiland, R.; Marru, S.; Pierce, M.; and Welch, V. Technical Report 2014.
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A credential store for multi-tenant science gateways. Kanewala, T., A.; Marru, S.; Basney, J.; and Pierce, M. In Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on, pages 445-454, 2014.
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Who Cares about Science Gateways? A Large-Scale Survey of Community Use and Needs. Lawrence, K., A.; Wilkins-Diehr, N.; Wernert, J., A.; Pierce, M.; Zentner, M.; and Marru, S. In 2014 9th Gateway Computing Environments Workshop, pages 1-4, 11 2014. IEEE
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Differential retention and divergent resolution of duplicate genes following whole-genome duplication. McGrath, C., L.; Gout, J.; Johri, P.; Doak, T., G.; and Lynch, M. Genome Research, 24(10): 1665-1675. 2014.
Differential retention and divergent resolution of duplicate genes following whole-genome duplication [link]Website   doi   link   bibtex   abstract  
De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) -- The Dominant Zooplankter of the North Atlantic Ocean. Lenz, P., H.; Roncalli, V.; Hassett, R., P.; Wu, L.; Cieslak, M., C.; Hartline, D., K.; and Christie, A., E. PLOS ONE, 9. 2014.
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National Center for Genome Analysis Program Year 2 Report - September 15, 2012 - September 14, 2013. Barnett. W. K., LeDuc, R. D., Stewart, C., A.; Barnett, W., K.; LeDuc, R., D.; and Stewart, C., A. Technical Report NATIONAL CENTER FOR GENOME ANALYSIS, 2014.
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Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. Peng, X.; Pipes, L.; Xiong, H.; Green, R., R.; Jones, D., C.; Ruzzo, W., L.; Schroth, G., P.; Mason, C., E.; Palermo, R., E.; and Katze, M., G. JOURNAL OF MEDICAL PRIMATOLOGY. 2014.
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Development of Single Nucleotide Polymorphism (SNP) Markers from the Mango (Mangifera indica ) Transcriptome for Mapping and Estimation of Genetic Diversity. Kuhn, D., N.; Dillon, N., L.; Innes, D., J.; Wu, L., S.; and Mockaitis, K. PLANT AND ANIMAL GENOME XXII CONFERENCE, 2014.
Development of Single Nucleotide Polymorphism (SNP) Markers from the Mango (Mangifera indica ) Transcriptome for Mapping and Estimation of Genetic Diversity [link]Website   link   bibtex  
Leveraging the national cyberinfrastructure for biomedical research. LeDuc, R.; Vaughn, M.; Fonner, J., M.; Sullivan, M.; Williams, J., G.; Blood, P., D.; Taylor, J.; and Barnett, W. Journal of the American Medical Informatics Association, 21(2): 195-199. 2014.
Leveraging the national cyberinfrastructure for biomedical research [pdf]Paper   doi   link   bibtex   abstract  
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. McGrath, C., L.; Gout, J.; Doak, T., G.; Yanagi, A.; and Lynch, M. Genetics, 197(4): 1417-1428. 2014.
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence [link]Website   doi   link   bibtex   abstract  
The mitochondrial genome of a Solanaceae cybrid plant is highly chimeric and retains a single form of most genes. Sanchez-Puerta, M., V.; Zubko, M.; and Palmer, J., D. GENOME RESEARCH. 2014.
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Expanding the catalog of cas genes with metagenomes. Zhang, Q.; Doak, T., G.; and Ye, Y. Nucleic Acids Research, 42(4): 2448-2459. 2014.
Expanding the catalog of cas genes with metagenomes [link]Website   doi   link   bibtex   abstract  
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Chen, X.; Bracht, J., R.; Goldman, A., D.; Dolzhenko, E.; Clay, D., M.; Swart, E., C.; Perlman, D., H.; Doak, T., G.; Stuart, A.; Amemiya, C., T.; Sebra, R., P.; and Landweber, L., F. Cell, 158(5): 1187-1198. 2014.
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development [link]Website   doi   link   bibtex   abstract  
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. Long, H.; Sung, W.; Miller, S., F.; Ackerman, M., S.; Doak, T., G.; and Lynch, M. Genome Biology and Evolution, 7(1): 262-271. 2014.
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948 [link]Website   doi   link   bibtex   abstract  
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Neale, D.; Wegrzyn, J.; Stevens, K.; Zimin, A.; Puiu, D.; Crepeau, M.; Cardeno, C.; Koriabine, M.; Morris, A., H.; Liechty, J.; Garcia, P., M.; Gross, H., V.; Lin, B.; and Zieve, J. GENOME BIOLOGY, 15. 2014.
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Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight. Blood, P., D.; Marcus, S.; and Schatz, M., C. In XSEDE 14 CONFERENCE PROCEEDINGS, 2014.
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The Encrypted Germline Genome of the Ciliate Oxytricha: A Paragon of Genome Rearrangement. Chen, X., Bracht, J.R., Goldman, A.D., Dolzhenko, E., Swart, E.C., Clay, D.M., Perlman, D.H., Doak, T.G., Stuart, A., Amemiya, C.T, Landweber, L.; Chen, X.; Bracht, J., R.; Goldman, A., D.; Dolzhenko, E.; Swart, E., C.; Clay, D., M.; Perlman, D., H.; Doak, T., G.; Stuart, A.; Amemiya, C., T.; and Landweber, L., F. MIC. 2014.
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The C-score: a bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. LeDuc, R., D.; Fellers, R., T.; Early, B., P.; Greer, J., B.; Thomas, P., M.; and Kelleher, N., L. JOURNAL OF PROTEOME RESEARCH, 13: 3231-3324. 2014.
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Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation. Wegrzyn, J., L.; Liechty, J., D.; Stevens, K., A.; Wu, L.; Loopstra, C., A.; Vasquez-Gross, H., A.; Dougherty, W., M.; Lin, B., Y.; Zieve, J., J.; Mart\'\inez-Garc\'\ia, P., J.; Holt, C.; and Y Genetics, 196: 891-909. 2014.
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Diversity and dynamics of the Drosophila transcriptome. Brown, J., B.; Boley, N.; Eisman, R.; May, G., E.; Stoiber, M., H.; Duff, M., O.; Booth, B., W.; Wen, J.; Park, S.; Suzuki, A., M.; Wan, K., H.; Yu, C.; Zhang, D.; and Carlson, J., W. of NATURE 2014.
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IEEE Cluster 2013 Conference final report-hosted by Indiana University Pervasive Technology Institute. Ping, R., J.; Miller, T.; Wernert, E., A.; and Stewart, C., A. Technical Report 2014.
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OASIS: a data and software distribution service for Open Science Grid. Bockelman, B.; Caballero, J.; De Stefano, J.; Hover, J.; Quick, R., E.; and Teige, S. Journal of Physics: Conference Series 513. 2014.
OASIS: a data and software distribution service for Open Science Grid [link]Website   doi   link   bibtex  
Models for Sustainability for Robust Cyberinfrastructure Software-Software Sustainability Survey. Wernert, J.; Wernert, E.; and Stewart, C. Technical Report 2014.
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XSEDE Campus Bridging Pilot Case Study. Hallock, B.; Knepper, R.; Ferguson, J.; and Stewart, C. In Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, pages 1-5, 2014. ACM Press
XSEDE Campus Bridging Pilot Case Study [link]Website   doi   link   bibtex   abstract  
Accelerating Sparse Canonical Correlation Analysis for Large Brain Imaging Genetics Data. Yan, J.; Zhang, H.; Du, L.; Wernert, E., A.; Saykin, A., J.; and Shen, L. In Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, 2014. ACM
Accelerating Sparse Canonical Correlation Analysis for Large Brain Imaging Genetics Data [link]Website   link   bibtex  
Visualization on Spherical Displays: Challenges and Opportunities. Vega, K.; Wernert, E.; Beard, P.; Gniady, C.; Reagan, D.; Boyles, M.; and Eller, C. In IEEE VIS 2014 Arts Program, 2014.
Visualization on Spherical Displays: Challenges and Opportunities [pdf]Website   link   bibtex  
ODI-portal, pipeline, and archive (ODI-PPA): A web-based astronomical compute archive, visualization, and analysis service. Gopu, A.; Hayashi, S.; Young, M., D.; Harbeck, D., R.; Boroson, T.; Liu, W.; Kotulla, R.; Shaw, R.; Henschel, R.; Rajagopal, J.; Stobie, E.; Knezek, P.; Martin, R., P.; and Archbold, K. In Proceedings of SPIE - The International Society for Optical Engineering, volume 9152, 2014. SPIE
ODI-portal, pipeline, and archive (ODI-PPA): A web-based astronomical compute archive, visualization, and analysis service [link]Website   doi   link   bibtex   abstract  
Comparison of multi-sample variant calling methods for whole genome sequencing. Nho, K.; West, J., D.; Li, H.; Henschel, R.; Tavares, M., C.; Bharthur, A.; Weiner, M., W.; Green, R., C.; Toga, A., W.; and Saykin, A., J. International Conference on Systems Biology, ISB,59-62. 2014.
Comparison of multi-sample variant calling methods for whole genome sequencing [link]Website   doi   link   bibtex   abstract  
Data Management Strategies for Scientific Applications in Cloud Environments. Ghoshal, D.; Hendrix, V.; Feller, E.; Morin, C.; Plale, B.; and Ramakrishnan, L. Technical Report 2014.
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Explicit semantic path mining via Wikipedia knowledge tree. Xia, T.; Chen, M.; and Liu, X. Proceedings of the ASIST Annual Meeting, 51(1). 2014.
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HPDC 2014 chairs' message. Plale, B.; Cappello, F.; Ripeanu, M.; and Xu, D. In HPDC 2014 - Proceedings of the 23rd International Symposium on High-Performance Parallel and Distributed Computing, 2014.
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Software Defined Multicasting for MPI Collective Operation Offloading with the NetFPGA BT - Euro-Par 2014 Parallel Processing: 20th International Conference, Porto, Portugal, August 25-29, 2014. Proceedings. Arap, O.; Brown, G.; Himebaugh, B.; and Swany, M. Volume 8632 LNCS . Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 632-643. Silva, F.; Dutra, I.; and Santos Costa, V., editor(s). Springer International Publishing, 2014.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) [link]Website   doi   link   bibtex   abstract  
Cloud computing data capsules for non-consumptiveuse of texts. Zeng, J.; Ruan, G.; Crowell, A.; Prakash, A.; and Plale, B. In Proceedings of the 5th ACM workshop on Scientific cloud computing, pages 9-16, 2014. ACM
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Synthesis of working group and interest group activity one year into the research data alliance. Plale, B. D-Lib Magazine, 20(1-2). 2014.
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Multi-tenant fair share in NoSQL data stores. Zeng, J.; and Plale, B. In 2014 IEEE International Conference on Cluster Computing, CLUSTER 2014, 2014.
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Parallel and quantitative sequential pattern mining for large-scale interval-based temporal data. Ruan, G.; Zhang, H.; and Plale, B. In Big Data (Big Data), 2014 IEEE International Conference on, pages 32-39, 2014. IEEE
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Indiana University Digitization Master Plan. Lewis, D.; and Plale, B. Technical Report 2014.
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Characterization of Emergent Data Networks Among Long-Tail Data. Elag, M.; Kumar, P.; Hedstrom, M.; Myers, J.; Plale, B.; Marini, L.; and McDonald, R. In EGU General Assembly Conference Abstracts, volume 16, 2014.
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DDDAS-Parallel Simulation of Threat Management in Urban Water Distribution Systems for Cloud Computing. Wang, L.; and von Laszewski, G. Computing in Science & Engineering, 16(1). 2014.
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The FutureGrid Testbed for Big Data. Von Laszewski, G.; and Fox, G., C. Cloud Computing for Data-Intensive Applications, pages 27-59. Springer, 2014.
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Towards a scientific impact measuring framework for large computing facilities - A case study on XSEDE. Wang, F.; Von Laszewski, G.; Fox, G., C., G.; Furlani, T.; DeLeon, R.; and Gallo, S. In ACM International Conference Proceeding Series, 2014.
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Accessing multiple clouds with Cloudmesh. Von Laszewski, G.; Wang, F.; Lee, H.; Chen, H.; and Fox, G., C., G. In BigSystem 2014 - Proceedings of the 2014 ACM International Workshop on Software-Defined Ecosystems, Co-located with HPDC 2014, 2014.
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Towards understanding cloud usage through resource allocation analysis on xsede. Lee, H.; von Laszewski, G.; Wang, F.; and Fox, G., C. Technical Report 2014.
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Comprehensive, open-source resource usage measurement and analysis for HPC systems. Browne, J.; Deleon, R.; Patra, A.; Barth, W.; Hammond, J.; Jones, M.; Furlani, T.; Schneider, B.; Gallo, S.; Ghadersohi, A.; Gentner, R.; Palmer, J.; Simakov, N.; Innus, M.; Bruno, A.; White, J.; Cornelius, C.; Yearke, T.; Marcus, K.; Von Laszewski, G.; and Wang, F. Concurrency Computation Practice and Experience, 26(13). 2014.
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Optimizing LZSS compression on GPGPUs. Ozsoy, A.; Swany, M.; and Chauhan, A. Future Generation Computer Systems, 30(1). 2014.
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Author gender metadata augmentation of hathitrust digital library. Peng, Z.; Chen, M.; Kowalczyk, S.; and Plale, B. Proceedings of the ASIST Annual Meeting, 51(1). 2014.
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Temporal representation for mining scientific data provenance. Chen, P.; Plale, B.; and Aktas, M. Future Generation Computer Systems, 36. 2014.
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Regenerating and Quantifying Quality of Benchmarking Data Using Static and Dynamic Provenance. Ghoshal, D.; Chauhan, A.; and Plale, B. In International Provenance and Annotation Workshop, pages 56-67, 2014. Springer
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Semantic annotation with RescoredESA: Rescoring concept features generated from explicit semantic analysis. Jiang, Z.; Chen, M.; and Liu, X. In ESAIR 2014 - Proceedings of the 7th International Workshop on Exploiting Semantic Annotations in Information Retrieval, co-located with CIKM 2014, 2014.
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Hierarchical MapReduce: Towards simplified cross-domain data processing. Luo, Y.; Plale, B.; Guo, Z.; Li, W.; Qiu, J.; and Sun, Y. Concurrency Computation Practice and Experience, 26(4). 2014.
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Executing Storm Surge Ensembles on PAAS Cloud. Chakraborty, A.; Pathirage, M.; Suriarachchi, I.; Chandrasekar, K.; Mattocks, C.; and Plale, B. Cloud Computing for Data-Intensive Applications, pages 257-276. Springer, 2014.
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Fast longest common subsequence with general integer scoring support on GPUs. Ozsoy, A.; Chauhan, A.; and Swany, M. In Proceedings of the 2014 International Workshop on Programming Models and Applications for Multicores and Manycores, PMAM 2014, 2014.
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Study in usefulness of middleware-only provenance. Zhou, Q.; Ghoshal, D.; and Plale, B. In Proceedings - 2014 IEEE 10th International Conference on eScience, eScience 2014, volume 1, 2014.
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Software Defined Multicasting for MPI Collective Operation Offloading with the NetFPGA. Arap, O.; Brown, G.; Himebaugh, B.; and Swany, M. 2014.
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Provenance quality assessment methodology and framework. Cheah, Y.; and Plale, B. Journal of Data and Information Quality, 5(3). 2014.
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Implementing mpi_barrier with the netfpga. Arap, O.; Brown, G.; Himebaugh, B.; and Swany, M. In Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA), pages 1, 2014. The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp)
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Apache Airavata: Design and Directions of a Science Gateway Framework. Pierce, M., E.; Marru, S.; Gunathilake, L.; Kanewala, T., A.; Singh, R.; Wijeratne, S.; Wimalasena, C.; Herath, C.; Chinthaka, E.; Mattmann, C.; Slominski, A.; Tangchaisin, P.; Wijeratne, D., K.; Singh, R.; Wimalasena, C.; Ratnayaka, S.; Pamidighantam, S.; Kanewala, T., A.; Singh, R.; Wijeratne, S.; Wimalasena, C.; Herath, C.; Chinthaka, E.; Mattmann, C.; Slominski, A.; and Tangchaisin, P. In 2014 6th International Workshop on Science Gateways, volume 27, pages 48-54, 6 2014. IEEE
Apache Airavata: Design and Directions of a Science Gateway Framework [link]Website   doi   link   bibtex   abstract  
Cloud computing for geodetic imaging data processing, analysis, and modeling. Donnellan, A.; Parker, J., W.; Wang, J.; Ma, Y.; and Pierce, M. In Aerospace Conference, 2014 IEEE, pages 1-9, 2014.
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Applications of E-DECIDER Decision Support Tools for Disaster Response and Recovery. Glasscoe, M., T.; Parker, J., W.; Wang, J.; Pierce, M., E.; Yoder, M., R.; Eguchi, R., T.; Huyck, C., K.; Hu, Z.; Bevington, J.; Ghosh, S.; and others 2014.
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Science Gateways, Scientific Workflows and Open Community Software. Pierce, M., E.; and Marru, S. In AGU Fall Meeting Abstracts, 2014.
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Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures. Memon, S.; Riedel, M.; Janetzko, F.; Demeler, B.; Gorbet, G.; Marru, S.; Grimshaw, A.; Gunathilake, L.; Singh, R.; Attig, N.; and Lippert, T. Concurrency and Computation: Practice and Experience, 26(13): 2280-2291. 9 2014.
Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures [link]Website   doi   link   bibtex   abstract  
WSSSPE2: Patching it up, pulling it forward. Pierce, M., E.; Marru, S.; and Mattmann, C. Journal of Open Research Software, 1112540(1). 2014.
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Globus Data Sharing: Security Assessment. Heiland, R.; Koranda, S.; and Welch, V. Technical Report 2014.
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Taking Stock After Four Years. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 4(2). 2014.
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Report of the 2013 NSF Cybersecurity Summit for Cyberinfrastructure and Large Facilities: Designing Cybersecurity Programs in Support of Science. Jackson, C.; Marsteller, J.; and Welch, V. Technical Report 2014.
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The Case for an Open and Evolving Software Assurance Framework. Livny, M.; Miller, B., P.; and Welch, V. In Proceedings of the International Conference on Software Engineering Research and Practice (SERP), pages 1, 2014. The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp)
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Systematic Government Access to Private-Sector Data Redux. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law. 2014.
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Building a data sharing model for global genomic research. Kosseim, P.; Dove, E., S.; Baggaley, C.; Meslin, E., M.; Cate, F., H.; Kaye, J.; Harris, J., R.; and Knoppers, B., M. Genome biology, 15(8): 430. 2014.
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When Two Worlds Collide: The Interface Between Competition Law and Data Protection. Cate, F., H.; Kuner, C.; Millard, C.; Svantesson, D., J., B.; and Lynskey, O. International Data Privacy Law, 4(4): 247-248. 2014.
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Report of the 2014 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure Large Facility Cybersecurity Challenges and Responses August 26‐August 28. Jackson, C.; Marsteller, J.; and Welch, V. Technical Report 2014.
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The (Data Privacy) Law Hasn't Even Checked in When Technology Takes Off. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 4(3): 175-176. 2014.
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Report of the 2014 NSF Cybersecurity Summit for Large Facilities and Cyberinfrastructure. Jackson, C.; Marsteller, J.; and Welch, V. Technical Report 2014.
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E-science infrastructures for molecular modeling and parametrization. Shen, N.; Fan, Y.; and Pamidighantam, S. Journal of Computational Science, 5(4): 576-589. 7 2014.
E-science infrastructures for molecular modeling and parametrization [pdf]Paper   E-science infrastructures for molecular modeling and parametrization [link]Website   doi   link   bibtex   abstract  
Performance improvement and workflow development of virtual diffraction calculations. Coleman, S., P.; Pamidighantam, S.; Koesterke, L.; Van Moer, M.; Spearot, D., E.; and Wang, Y. In Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment (XSEDE '14), 2014. Association for Computing Machinery
Performance improvement and workflow development of virtual diffraction calculations [pdf]Paper   doi   link   bibtex   abstract  
Methods For Creating XSEDE Compatible Clusters. Fischer, J.; Knepper, R.; Standish, M.; Stewart, C., A.; Alvord, R.; Lifka, D.; Hallock, B.; and Hazlewood, V. In Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE '14, pages 1-5, 2014. ACM Press
Methods For Creating XSEDE Compatible Clusters [link]Website   doi   link   bibtex   abstract  
A case study: Holistic performance analysis on heterogeneous architectures using the vampir toolchain. Dietrich, R.; Winkler, F.; William, T.; Stolle, J.; Henschel, R.; and Berry, D., K. Advances in Parallel Computing, 25: 793-802. 2014.
A case study: Holistic performance analysis on heterogeneous architectures using the vampir toolchain [link]Website   doi   link   bibtex   abstract  
Making campus bridging work for researchers: Can campus bridging experts accelerate discovery?. Michael, S.; Thota, A.; Henschel, R.; and Knepper, R. Concurrency Computation Practice and Experience, 26(13): 2141-2148. 2014.
Making campus bridging work for researchers: Can campus bridging experts accelerate discovery? [link]Website   doi   link   bibtex   abstract  
Leveraging Your Local Resources and National Cyberinfrastructure Resources without Tears. Hallock, B.; Knepper, R.; Ferguson, J.; and Stewart, C., A. In Proceedings of the 2014 ACM SIGUCCS Annual Conference on User Services Conference - SIGUCCS '14, pages 107-110, 2014. ACM Press
Leveraging Your Local Resources and National Cyberinfrastructure Resources without Tears [link]Website   doi   link   bibtex   abstract  
Corrigendum: Systems survey of endocytosis by multiparametric image analysis (Nature (2010) 464, (243-249) DOI: 10.1038/nature08779). Collinet, C.; Stöter, M.; Bradshaw, C., R.; Samusik, N.; Rink, J., C.; Kenski, D.; Habermann, B.; Buchholz, F.; Henschel, R.; Mueller, M., S.; Nagel, W., E.; Fava, E.; Kalaidzidis, Y.; and Zerial, M. Nature, 513(7518): 444. 2014.
Corrigendum: Systems survey of endocytosis by multiparametric image analysis (Nature (2010) 464, (243-249) DOI: 10.1038/nature08779) [link]Website   doi   link   bibtex  
Sustainability of cyberinfrastructure software: Community needs, case studies, and success strategies. Stewart, C., A.; Barnett, W., K.; Wernert, E., A.; Wernert, J., A.; Welch, V.; and Knepper, R. Technical Report 2014.
Sustainability of cyberinfrastructure software: Community needs, case studies, and success strategies [link]Website   link   bibtex   abstract  
Galaxy based BLAST submission to distributed national high throughput computing resources. Hayashi, S.; Gesing, S.; Quick, R.; Teige, S.; Ganote, C.; Wu, L.; and Prout, E. In Proceedings of Science, volume 23-28-Marc, 2014. Proceedings of Science (PoS)
Galaxy based BLAST submission to distributed national high throughput computing resources [link]Website   link   bibtex   abstract  
The role of the collaboratory in enabling large-scale identity management for HEP. Cowles, R.; Jackson, C.; and Welch, V. Journal of Physics: Conference Series, 513(TRACK 3). 2014.
The role of the collaboratory in enabling large-scale identity management for HEP [link]Website   doi   link   bibtex   abstract  
OSG PKI transition: Experiences and lessons learned. Welch, V.; Deximo, A.; Hayashi, S.; Khadke, V., D.; Mathure, R.; Quick, R.; Altunay, M.; Sehgal, C., S.; Tiradani, A.; and Basney, J. In Proceedings of Science, volume 23-28-Marc, 2014. Proceedings of Science (PoS)
OSG PKI transition: Experiences and lessons learned [link]Website   link   bibtex   abstract  
GenApp module execution and airavata integration. Brookes, E., H.; Anjum, N.; Curtis, J., E.; Marru, S.; Singh, R.; and Pierce, M. In Proceedings of the 9th Gateway Computing Environments Workshop, pages 9-12, 2014. Institute of Electrical and Electronics Engineers Inc.
GenApp module execution and airavata integration [link]Website   doi   link   bibtex   abstract  
A model for identity management in future scientific collaboratories. Cowles, R.; Jackson, C.; Welch, V.; and Cholia, S. In Proceedings of Science, volume 23-28-Marc, 2014. Proceedings of Science (PoS)
A model for identity management in future scientific collaboratories [link]Website   link   bibtex   abstract  
XSEDE 12 Conference Final Report. Stewart, C., A.; Miller, T.; Blood, P.; Tillotson, J.; Froelich, W.; DeStefano, L.; and Rivera, L. Technical Report 7 2014.
XSEDE 12 Conference Final Report [pdf]Paper   XSEDE 12 Conference Final Report [link]Website   link   bibtex  
National Center for Genome Analysis Program Year 3 Report - September 15, 2013 - September 14, 2014. Barnett, W., K.; Doak, T., G.; and Stewart, C., A. Technical Report 2014.
National Center for Genome Analysis Program Year 3 Report - September 15, 2013 - September 14, 2014 [pdf]Paper   National Center for Genome Analysis Program Year 3 Report - September 15, 2013 - September 14, 2014 [link]Website   link   bibtex   abstract  
2013 annual report on training, education, and outreach activities of the Indiana University Pervasive Technology Institute and affiliated organizations. Ping, R., J.; Miller, T.; Plale, B.; and Stewart, C. Technical Report 2014.
2013 annual report on training, education, and outreach activities of the Indiana University Pervasive Technology Institute and affiliated organizations [pdf]Paper   2013 annual report on training, education, and outreach activities of the Indiana University Pervasive Technology Institute and affiliated organizations [link]Website   link   bibtex   abstract  
Economic development by the Indiana University Pervasive Technology Institute, Pervasive Technology Labs, and the Research Technologies Division of University Information Technology Services during FY 2012/2013. Miller, T.; and Stewart, C., A. Technical Report 9 2014.
Economic development by the Indiana University Pervasive Technology Institute, Pervasive Technology Labs, and the Research Technologies Division of University Information Technology Services during FY 2012/2013 [link]Website   link   bibtex  
  2013 (132)
Hybrid MPI: efficient message passing for multi-core systems. Friedley, A.; Bronevetsky, G.; Hoefler, T.; and Lumsdaine, A. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, pages 18, 2013. ACM
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Ownership passing: Efficient distributed memory programming on multi-core systems. Friedley, A.; Hoefler, T.; Bronevetsky, G.; Lumsdaine, A.; and Ma, C. In ACM SIGPLAN Notices, volume 48, pages 177-186, 2013. ACM
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Expressing graph algorithms using generalized active messages. Edmonds, N.; Willcock, J.; and Lumsdaine, A. In Proceedings of the 27th international ACM conference on International conference on supercomputing, pages 283-292, 2013. ACM
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GPU programming in rust: Implementing high-level abstractions in a systems-level language. Holk, E.; Pathirage, M.; Chauhan, A.; Lumsdaine, A.; and Matsakis, N., D. In Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 2013 IEEE 27th International, pages 315-324, 2013. IEEE
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Compiled MPI: Cost-Effective Exascale Application Development. Lumsdaine, A.; and Friedley, A. Technical Report 2013.
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Hybrid MPI: Efficient Message Passing for Shared and Distributed Memory. Friedley, A.; Bronevetsky, G.; Hoefler, T.; and Lumsdaine, A. Technical Report 2013.
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Quantifying Program Complexity and Comprehension. Hansen, M.; Lumsdaine, A.; Goldstone, R.; Hill, R.; and Yu, C. Technical Report 2013.
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Award ER25750: Coordinated Infrastructure for Fault Tolerance Systems Indiana University Final Report. Lumsdaine, A. Technical Report 2013.
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Minimizing Exascale Memory Bandwidth Usage through Sparse Matrix Compression. Willcock, J.; and Lumsdaine, A. In Exascale Mathematics Working Group Workshop, 2013.
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Mobile Computational Photography 2013: Introduction to the JEI Focal Track Presentations. Georgiev, T.; and Lumsdaine, A. SPIE, 8667. 2013.
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Optimizing process creation and execution on multi-core architectures. Kulkarni, A.; Ionkov, L.; Lang, M.; and Lumsdaine, A. The International Journal of High Performance Computing Applications, 27(2): 147-161. 2013.
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Exascale computing. Gottlieb, S.; and Sterling, T. Computing in Science and Engineering, 15(6): 12-15. 2013.
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Data intensive computing for bioinformatics. Qiu, J.; Ekanayake, S.; Ekanayake, J.; Wu, S.; Gunarathne, T.; Beason, S.; Choi, Y.; Fox, G., C.; Bae, S.; Rho, M.; Ruan, Y.; and Tang, H. Volume 1 2013.
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Mammoth data in the cloud: Clustering social images. Qiu, J.; and Zhang, B. Volume 23 2013.
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Survey of Streaming Data Algorithms. Kamburugamuve, S.; Fox, G., C.; Leake, D.; and Qiu, J. Technical Report 2013.
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CINET Collaboration Report. WU, T., A., K., L., O., N., S.; Wiggins, T.; and Qiu, J. Technical Report 2013.
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Clustering Social Images with MapReduce and High Performance Collective Communication. Zhang, B.; and Qiu, J. High-Performance Parallel and Distributed Computing. 2013.
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Supporting end-to-end social media data analysis with the IndexedHBase platform. Gao, X.; and Qiu, J. In Proceedings of the 6th workshop on many-task computing on clouds, grids, and supercomputers (MTAGS) at SC13, 2013.
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Survey of apache big data stack. Kamburugamuve, S.; Fox, G., C.; Leake, D.; and Qiu, J. Indiana University, Tech. Rep.. 2013.
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Performance Modeling of Gyrokinetic Toroidal Simulations for a many-tasking runtime system. Anderson, M.; Brodowicz, M.; Kulkarni, A.; and Sterling, T. In International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems, pages 136-157, 2013. Springer
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Application characteristics of many-tasking execution models. Gilmanov, T.; Anderson, M.; Brodowicz, M.; and Sterling, T. In Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA), pages 263, 2013. The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp)
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Achieving scalability in the presence of Asynchrony for Exascale Computing. Sterling, T.; Anderson, M.; and Brodowicz, M. Transition of HPC Towards Exascale Computing, 24: 104. 2013.
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Towards brain-inspired system architectures. Sterling, T.; Brodowicz, M.; and Gilmanov, T. In International Workshop on Brain-Inspired Computing, pages 159-170, 2013. Springer
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Overplotting: Unified solutions under abstract rendering. Cottam, J.; Lumsdaine, A.; and Wang, P. In Big Data, 2013 IEEE International Conference on, pages 9-16, 2013. IEEE
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Toward a Research Software Security Maturity Model. Heiland, R.; Thomas, B.; Welch, V.; and Jackson, C. arXiv preprint arXiv:1309.1677. 2013.
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High performance clustering of social images in a map-collective programming model. Zhang, B.; and Qiu, J. In Proceedings of the 4th annual Symposium on Cloud Computing, pages 44, 2013. ACM
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Social media data analysis with IndexedHBase and iterative MapReduce. Gao, X.; and Qiu, J. In Proceedings of the 6th Workshop on Many-Task Computing on Clouds, Grids, and Supercomputers (MTAGS 2013), 2013.
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High-level Coordination Specification. Cottam, J., A.; Holk, E.; Byrd, W., E.; Chauhan, A.; and Lumsdaine, A. In Workshop on Leveraging Abstractions and Semantics in High-performance Computing (LASH-C), 2013.
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Tabulated equations of state with a many-tasking execution model. Anderson, M.; Brodowicz, M.; Sterling, T.; Kaiser, H.; and Adelstein-Lelbach, B. In Proceedings - IEEE 27th International Parallel and Distributed Processing Symposium Workshops and PhD Forum, IPDPSW 2013, pages 1691-1699, 2013. IEEE Computer Society
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Understanding the needs of low SES patients with type 2 diabetes. Barnes, P.; Caine, K.; Connelly, K.; and Siek, K. In Pervasive Computing Technologies for Healthcare (PervasiveHealth), 2013 7th International Conference on, pages 302-306, 2013. IEEE
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Connecting central shared file systems across the Open Science Grid and the European Grid Initiative. Teige, S.; Hayashi, S.; Quick, R.; Lee, T.; Prout, E.; Tavares, M.; and Deximo, A. In The International Symposium on Grids and Clouds (ISGC), volume 2013, 2013.
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How in-home technologies mediate caregiving relationships in later life. Huber, L., L.; Shankar, K.; Caine, K.; Connelly, K.; Camp, L., J.; Walker, B., A.; and Borrero, L. International Journal of Human-Computer Interaction, 29(7): 441-455. 2013.
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Using a mobile application to self‐monitor diet and fluid intake among adults receiving hemodialysis. Welch, J., L.; Astroth, K., S.; Perkins, S., M.; Johnson, C., S.; Connelly, K.; Siek, K., A.; Jones, J.; and Scott, L., L. Research in nursing & health, 36(3): 284-298. 2013.
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Designing for positive health affect: Decoupling negative emotion and health monitoring technologies. Toscos, T.; Connelly, K.; and Rogers, Y. In Proceedings of the 7th International Conference on Pervasive Computing Technologies for Healthcare, pages 153-160, 2013. ICST (Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering)
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Consumer engagement in health technologies special interest group. Cheng, K.; Caine, K.; Pratt, W.; and Connelly, K. In CHI'13 Extended Abstracts on Human Factors in Computing Systems, pages 2485-2488, 2013. ACM
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Formative evaluation of a mobile liquid portion size estimation interface for people with varying literacy skills. Chaudry, B., M.; Connelly, K.; Siek, K., A.; and Welch, J., L. Journal of ambient intelligence and humanized computing, 4(6): 779-789. 2013.
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Making sense of mobile-and web-based wellness information technology: cross-generational study. Kutz, D.; Shankar, K.; and Connelly, K. Journal of medical Internet research, 15(5). 2013.
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Enabling high performance computing in cloud infrastructure using virtualized GPUs. Younge, A., J.; Walters, J., P.; Crago, S.; and Fox, G., C. . 2013.
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Chaining Data and Visualization Web Services for Decision Making in Information Systems. Sayar, A.; and Pierce, M., E. In International Conference on Availability, Reliability, and Security, pages 44-53, 2013.
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US-SOMO Cluster Methods: Year One Perspective. Brookes, E.; Singh, R.; Pierce, M.; Marru, S.; Demeler, B.; and Rocco, M. In XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013. ACM
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Science Gateways. Pierce, M. 2013.
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Improvements of the ultrascan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures. Memon, S.; Attig, N.; Gorbet, G.; Gunathilake, L.; Riedel, M.; Lippert, T.; Marru, S.; Grimshaw, A.; Janetzko, F.; Demeler, B.; and Singh, R. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), pages 7, 2013.
Improvements of the ultrascan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures [link]Website   doi   link   bibtex   abstract  
QuakeSim data architecture and technology. Donnellan, A.; Glasscoe, M.; Parker, J.; Granat, R.; Pierce, M.; Wang, J.; Rundle, J.; Sachs, M.; and Ludwig, L., G. Technical Report 2013.
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Twitter bootstrap and AngularJS: Frontend frameworks to expedite science gateway development. Balasubramanee, V.; Wimalasena, C.; Singh, R.; and Pierce, M. In Cluster Computing (CLUSTER), 2013 IEEE International Conference on, pages 1, 2013.
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Science Gateway Operational Sustainability: Adopting a Platform-as-a Service Approach. Pierce, M.; Marru, S.; Miller, M., A.; Majumdar, A.; and Demeler, B. Technical Report 2013.
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Authoring a Science Gateway Cookbook. Marru, S.; Dooley, R.; Wilkins-Diehr, N.; Pierce, M.; Miller, M.; Pamidighantam, S.; and Wernert, J. In Cluster Computing (CLUSTER), 2013 IEEE International Conference on, pages 1-3, 2013.
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Science gateways and the importance of sustainability. Wilkins-Diehr, N.; Lawrence, K.; Hayden, L.; Pierce, M.; Marru, S.; McLennan, M.; Zentner, M.; Dooley, R.; and Stanzione, D. figshare,790764. 2013.
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E-DECIDER Decision Support Gateway For Earthquake Disaster Response. Glasscoe, M., T.; Stough, T., M.; Parker, J., W.; Burl, M., C.; Donnellan, A.; Blom, R., G.; Pierce, M., E.; Wang, J.; Ma, Y.; Rundle, J., B.; and others In AGU Fall Meeting Abstracts, 2013.
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Sustainable cyberinfrastructure software through open governance. Pierce, M.; Marru, S.; and Mattmann, C. Technical Report 2013.
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National center for genome analysis support leverages XSEDE to support life science research. Leduc, R., D.; Wu, L.; Ganote, C., L.; Doak, T.; Blood, P., D.; Vaughn, M.; and LeDuc, R., Wu, L.-S., Ganote, C., Doak, T., Blood, P., Vaughn, M., and Williams, B. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), 2013.
National center for genome analysis support leverages XSEDE to support life science research [link]Website   doi   link   bibtex   abstract  
Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate. Jin, M.; Bothfeld, W.; Austin, S.; Sato, T., K.; Alex, L., R.; Li, H.; Foston, M.; Gunawan, C.; LeDuc, R., D.; Quensen, J., F.; McGee, M.; Uppugundla, N.; Higbee, A.; and Ranatu BIORESOURCE TECHNOLOGY, 147: 212-220. 2013.
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The gain and loss of chromosomal integron systems in the Treponema species. Wu, Y.; Doak, T., G.; and Ye, Y. BMC Evolutionary Biology, 13(1). 2013.
The gain and loss of chromosomal integron systems in the Treponema species [link]Website   doi   link   bibtex   abstract  
Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula. Stanton-Geddes, J.; Paape, T.; Epstein, B.; Briskine, R.; Yoder, J.; Mudge, J.; Bharti, A., K.; Farmer, A., D.; Zhou, P.; Denny, R.; May, G., D.; Erlandson, S.; and Yakub, M. PLOS ONE, 8. 2013.
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The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Pipes, L.; Li, S.; Bozinoski, M.; Palermo, R.; Peng, X.; Blood, P.; Kelly, S.; Weiss, J., M.; Thierry-Mieg, J.; Thierry-Mieg, D.; Zumbo, P.; Chen, R.; Schroth, G., P.; Mason, C., E.; and Katze, M., G. NUCLEIC ACIDS RES, 41: D906-14. 2013.
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Statistical Consideration for Identification and Quantification in Top-Down Proteomics. LeDuc, R. In American Society for Mass Spectrometry, Sanibel Conference 2013, 2013.
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Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. Christie, A.E., Roncalli, V., Wu, L.-S., Ganote, C.L., Doak, T.G., Lenz, P.; Christie, A., E.; Roncalli, V.; Wu, L.; Ganote, C., L.; Doak, T.; and Lenz, P., H. General and Comparative Endocrinology, 187: 117-135. 2013.
Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome [link]Website   doi   link   bibtex  
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Boscaro, V.; Felletti, M.; Vannini, C.; Ackerman, M., S.; Chain, P., S., G.; Malfatti, S.; Vergez, L., M.; Shin, M.; Doak, T., G.; Lynch, M.; and Petroni, G. Proceedings of the National Academy of Sciences of the United States of America, 110(46): 18590-18595. 2013.
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria [link]Website   doi   link   bibtex   abstract  
Towards Virtual Computational Facilities for Genomics Research: How 100 Gbps Networking Will Change Bioinformatics. Barnett, W., Michael, S., Wu, L.-S., LeDuc, R., Doak, T. In eScience 2013, 2013.
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The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating traits: pod color as an example". Motamayor, J. C., Mockaitis, K., Schmutz, J., e., a., (., G., G.; Motamayor, J., C.; Mockaitis, K.; Schmutz, J.; Haiminen, N.; Donald; Cornejo, O.; Findley, S.; Zheng, P.; Utro, F.; Royaert, S.; Saski, C.; Jenkins, J.; Podicheti, R.; Zhao, M.; Motamayor, J. C., Mockaitis, K., Schmutz, J., e., a., (., G., G.; Motamayor, J., C.; Mockaitis, K.; Schmutz, J.; Haiminen, N.; Donald; Cornejo, O.; Findley, S.; Zheng, P.; Utro, F.; Royaert, S.; Saski, C.; Jenkins, J.; Podicheti, R.; Zhao, M.; and others Genome Biology, 14. 2013.
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Spliced DNA sequences in the Paramecium germline: Their properties and evolutionary potential. Catania, F.; McGrath, C., L.; Doak, T., G.; and Lynch, M. Genome Biology and Evolution, 5(6): 1200-1211. 2013.
Spliced DNA sequences in the Paramecium germline: Their properties and evolutionary potential [link]Website   doi   link   bibtex   abstract  
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. Zhang, Q.; Rho, M.; Tang, H.; Doak, T., G.; and Ye, Y. Genome Biology, 14(4). 2013.
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes [link]Website   doi   link   bibtex   abstract  
A genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria. Raymann, K.; Bobay, L.; Doak, T., G.; Lynch, M.; and Gribaldo, S. G3: Genes, Genomes, Genetics, 3(3): 505-516. 2013.
A genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria [link]Website   doi   link   bibtex   abstract  
National Center for Genome Analysis Program Year 1 Report - September 15, 2011 - September 14, 2012. Barnett, W.; Ganote, C.; Vaughn, M.; LeDuc, R., D.; and Stewart, C., A. Technical Report 2013.
National Center for Genome Analysis Program Year 1 Report - September 15, 2011 - September 14, 2012 [link]Website   link   bibtex   abstract  
Reply to massey: Drift does influence mutation-rate evolution. Sung, W.; Ackerman, M., S.; Miller, S., F.; Doak, T., G.; and Lynch, M. Proceedings of the National Academy of Sciences of the United States of America, 110(10): E860. 2013.
Reply to massey: Drift does influence mutation-rate evolution [link]Website   doi   link   bibtex  
Expanding the Catalog of Cas Proteins by Metagenomes. Zhang, Q., Doak, T.G., Rho, M., Ye, Y. PLoS CB. 2013.
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The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Youssef, N., H.; Couger, M., B.; Struchtemeyer, C., G.; Liggenstoffer, A., S.; Prade, R., A.; Najar, F., Z.; Atiyeh, H., K.; Wilkins, M., R.; and Elshahed, M., S. APPL ENVIRON MICROBIOL, 79: 4620-4634. 2013.
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The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. Swart, E., C.; Bracht, J., R.; Magrini, V.; Minx, P.; Chen, X.; Zhou, Y.; Khurana, J., S.; Goldman, A., D.; Nowacki, M.; Schotanus, K.; Jung, S.; Fulton, R., S.; Ly, A.; McGrath, S.; Haub, K.; Wiggins, J., L.; Storton, D.; Matese, J., C.; Parsons, L.; Chang, W.; Bowen, M., S.; Stover, N., A.; Jones, T., A.; Eddy, S., R.; Herrick, G., A.; Doak, T., G.; Wilson, R., K.; Mardis, E., R.; and Landweber, L., F. PLoS Biology, 11(1). 2013.
The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes [link]Website   doi   link   bibtex   abstract  
XSEDE Campus Bridging–Cluster software distribution strategy and tactics. Hazlewood, V.; Knepper, R.; Lee, S.; Lifka, D.; Navarro, J., P.; and Stewart, C., A. Technical Report 2013.
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Initial findings from a study of best practices and models for cyberinfrastructure software sustainability. Stewart, C., A.; Wernert, J.; Wernert, E., A.; Barnett, W., K.; and Welch, V. arXiv preprint arXiv:1309.1817. 2013.
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Performance evaluation of R with Intel Xeon Phi Coprocessor. El-Khamra, Y.; Gaffney, N.; Walling, D.; Wernert, E., A.; Xu, W.; and Zhang, H. In 2013 IEEE International Conference on Big Data (IEEE Big Data 2013), 10 2013.
Performance evaluation of R with Intel Xeon Phi Coprocessor [link]Website   link   bibtex  
Visual exploration and analysis of human-robot interaction rules. Zhang, H.; and Boyles, M., J. In Wong, P., C.; Kao, D., L.; Hao, M., C.; Chen, C.; and Healey, C., G., editor(s), IS&T/SPIE Electronic Imaging conference, pages 86540E, 2 2013. Society of Photo-Optical Instrumentation Engineers (SPIE)
Visual exploration and analysis of human-robot interaction rules [link]Website   doi   link   bibtex   abstract  
Light curve of CR bootis 1990-2012 from the indiana long-term monitoring program. Honeycutt, R., K.; Adams, B., R.; Turner, G., W.; Robertson, J., W.; Ost, E., M.; and Maxwell, J., E. Publications of the Astronomical Society of the Pacific, 125(924): 126-142. 2013.
Light curve of CR bootis 1990-2012 from the indiana long-term monitoring program [link]Website   doi   link   bibtex   abstract  
Performance and quality of service of data and video movement over a 100 Gbps testbed. Kluge, M.; Simms, S.; William, T.; Henschel, R.; Georgi, A.; Meyer, C.; Mueller, M., S.; Stewart, C., A.; Wünsch, W.; and Nagel, W., E. Future Generation Computer Systems, 29(1): 230-240. 1 2013.
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DEM generation with SAR interferometry based on weighted wavelet phase unwrapping. Rahnemoonfar, M.; and Plale, B. In Proceedings - 2013 4th International Conference on Computing for Geospatial Research and Application, COM.Geo 2013, 2013.
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Modeling heterogeneous data resources for social-ecological research: A data-centric perspective. Chen, M.; Pavalanathan, U.; Jensen, S.; and Plale, B. In Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, 2013.
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Data pipeline in mapreduce. Zeng, J.; and Plale, B. In Proceedings - IEEE 9th International Conference on e-Science, e-Science 2013, 2013.
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Big Data and HPC: Exploring Role of Research Data Alliance (RDA), a Report On Supercomputing 2013 Birds of a Feather. Plale, B. Technical Report 2013.
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Provenance capture and use in a satellite data processing pipeline. Jensen, S.; Plale, B.; Aktas, M.; Luo, Y.; Chen, P.; and Conover, H. IEEE Transactions on Geoscience and Remote Sensing, 51(11). 2013.
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Standards for graph algorithm primitives. Mattson, T.; Bader, D.; Berry, J.; Buluc, A.; Dongarra, J.; Faloutsos, C.; Feo, J.; Gilbert, J.; Gonzalez, J.; and Hendrickson, B. In High Performance Extreme Computing Conference (HPEC), 2013 IEEE, pages 1-2, 2013. IEEE
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Storm surge simulation and load balancing in azure cloud. Chakraborty, A.; Pathirage, M.; Suriarachchi, I.; Chandrasekar, K.; Mattocks, C.; and Plale, B. In Simulation Series, volume 45, 2013.
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Milieu: Lightweight and configurable big data provenance for science. Cheah, Y.; Canon, R.; Plale, B.; and Ramakrishnan, L. In Proceedings - 2013 IEEE International Congress on Big Data, BigData 2013, 2013.
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Towards Tera-Scale Performance for Longest Common Subsequence Using Graphics Processor. Ozsoy, A.; Chauhan, A.; and Swany, M. IEEE Supercomputing (SC). 2013.
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Big Data Opportunities and Challenges for IR, Text Mining and NLP. Plale, B. In UnstructureNLP '13 Proceedings of the 2013 international workshop on Mining unstructured big data using natural language processing, volume Proceeding, 2013. ACM
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Exploiting mapreduce and data compression for data-intensive applications. Ruan, G.; Zhang, H.; and Plale, B. In ACM International Conference Proceeding Series, 2013.
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Changing the Curation Equation: A Data Lifecycle Approach to Lowering Costs and Increasing Value. Myers, J.; Hedstrom, M.; Plale, B., A.; Kumar, P.; McDonald, R.; Kooper, R.; Marini, L.; Kouper, I.; and Chandrasekar, K. In AGU Fall Meeting Abstracts, 2013.
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Big data at scale for digital humanities: An architecture for the hathitrust research center. Kowalczyk, S.; Sun, Y.; Peng, Z.; Plale, B.; Todd, A.; Auvil, L.; Willis, C.; Zeng, J.; Pathirage, M.; Liyanage, S.; Ruan, G.; and Stephen Downie, J. 2013.
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Unmanaged workflows: Their provenance and use. Aktas, M.; Plale, B.; Leake, D.; and Mukhi, N. Volume 426 2013.
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Data Sets, Ensemble Cloud Computing, and the University Library. Plale, B., A. In AGU Fall Meeting Abstracts, 2013.
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Design and Implementation of a Unified Network Information Service. El-Hassany, A.; Kissel, E.; Gunter, D.; and Swany, M. In Proceedings - IEEE 10th International Conference on Services Computing, SCC 2013, 2013.
Design and Implementation of a Unified Network Information Service [link]Website   doi   link   bibtex   abstract  
SEAD virtual archive: Building a federation of institutional repositories for long-term data preservation in sustainability science. Plale, B.; McDonald, R., H.; Chandrasekar, K.; Kouper, I.; Konkiel, S.; Hedstrom, M., L.; Myers, J.; and Kumar, P. International Journal of Digital Curation, 8(2): 172-180. 2013.
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Automatic performance evaluation of dewarping methods in large scale digitization of historical documents. Rahnemoonfar, M.; and Plale, B. In Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, 2013.
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Message from the research track chairs. Plale, B.; Lyu, M.; and Zhang, J. In Proceedings - IEEE 20th International Conference on Web Services, ICWS 2013, 2013.
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Performance metrics and auditing framework using application kernels for high-performance computer systems. Furlani, T.; Jones, M.; Gallo, S.; Bruno, A.; Lu, C.; Ghadersohi, A.; Gentner, R.; Patra, A.; Deleon, R.; Von Laszewski, G.; Wang, F.; and Zimmerman, A. Concurrency Computation Practice and Experience, 25(7). 2013.
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Co-processing SPMD computation on CPUs and GPUs cluster. Li, H.; Fox, G., C.; Von Laszewski, G.; and Chauhan, A. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, 2013.
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On-demand service hosting on production grid infrastructures. Wang, L.; Kurze, T.; Tao, J.; Kunze, M.; and Von Laszewski, G. Journal of Supercomputing, 66(3). 2013.
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Using XDMoD to facilitate XSEDE operations, planning and analysis. Furlani, T.; Schneider, B.; Jones, M.; Towns, J.; Hart, D.; Gallo, S.; Deleon, R.; Lu, C.; Ghadersohi, A.; Gentner, R.; Patra, A.; Laszewski, G.; Wang, F.; Palmer, J.; and Simakov, N. In ACM International Conference Proceeding Series, 2013.
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Static compiler analysis for workflow provenance. Ghoshal, D.; Chauhan, A.; and Plale, B. In Proceedings of WORKS 2013: 8th Workshop on Workflows in Support of Large-Scale Science - Held in conjunction with SC 2013: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2013.
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HathiTrust research center: computational access for digital humanities and beyond. Plale, B.; McDonald, R., H.; Sun, Y.; Kouper, I.; Cobine, R.; Downie, J., S.; Namachchivaya, B., B., S.; Unsworth, J.; Stephen Downie, J.; Namachchivaya, B., B., S.; and Unsworth, J. In Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, 2013. ACM
HathiTrust research center: computational access for digital humanities and beyond [link]Website   doi   link   bibtex   abstract  
Efficient wide area data transfer protocols for 100 Gbps networks and beyond. Kissel, E.; Swany, M.; Tierney, B.; and Pouyoul, E. In Proc. of NDM 2013: 3rd Int. Workshop on Network-Aware Data Management - Held in Conjunction with SC 2013: The Int. Conference for High Performance Computing, Networking, Storage and Analysis, 2013.
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Dependency provenance in agent based modeling. Chen, P.; Plale, B.; and Evans, T. In Proceedings - IEEE 9th International Conference on e-Science, e-Science 2013, 2013.
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The SEAD datanet prototype: Data preservation services for sustainability science. Plale, B.; McDonald, R.; Chandrasekar, K.; Kouper, I.; Light, R.; Konkiel, S.; Hedstrom, M.; Myers, J.; and Kumar, P. In Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, 2013.
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Provenance from log files: a BigData problem. Ghoshal, D.; and Plale, B. In Proceedings of the Joint EDBT/ICDT 2013 Workshops, pages 290-297, 2013. ACM
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Repository of NSF Funded Publications and Data Sets:" Back of Envelope" 15 year Cost Estimate. Plale, B.; Kouper, I.; McDonald, R.; Seiffert, K.; and Konkiel, S. Technical Report 2013.
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perfSONAR: On-board diagnostics for big data. Zurawski, J.; Balasubramanian, S.; Brown, A.; Kissel, E.; Lake, A.; Swany, M.; Tierney, B.; and Zekauskas, M. In IEEE International Conference on Big Data, 2013.
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Achieving TeraCUPS on Longest Common Subsequence Problem Using GPGPUs. Ozsoy, A.; Chauhan, A.; and Swany, M. In Parallel and Distributed Systems (ICPADS13), 2013 International Conference on, pages 69-77, 2013. IEEE
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Enabling Dark Energy Survey science analysis with simulations on XSEDE resources. Erickson, B., M., S.; Singh, R.; Evrard, A.; Becker, M., R.; Busha, M.; Kravtsov, A., V.; Marru, S.; Pierce, M.; and Wechsler, R., H. In XSEDE '13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013. ACM
Enabling Dark Energy Survey science analysis with simulations on XSEDE resources [link]Website   link   bibtex  
Integrating remotely sensed and ground observations for modeling, analysis, and decision support. Donnellan, A.; Glasscoe, M.; Parker, J., W.; Granat, R.; Pierce, M.; Wang, J.; Fox, G., C.; McLeod, D.; Rundle, J.; Heien, E.; and others In Aerospace Conference, 2013 IEEE, pages 1-12, 2013.
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Apache Airavata: Building Gateways to Innovation. Pierce, M.; Marru, S.; Wijeratne, S.; Singh, R.; and Suriyaarachchi, H. 2013.
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The Extraterritoriality of Data Privacy Laws--An Explosive Issue Yet to Detonate. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 3(3): 147-148. 2013.
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CyberGIS-CTSC Engagement Final Report. Butler, R.; Fleury, T.; Marsteller, J.; and Welch, V. Technical Report 2013.
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PRISM and Privacy: Will This Change Everything?. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 3(4): 217-219. 2013.
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HIPAA and Advanced Scientific Computing. Shankar, A.; and Barnett, W. Technical Report 2013.
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The Business of Privacy. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law. 2013.
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Notice and Consent in a World of Big Data. Cate, F., H.; and Mayer-Schonberger, V. International Data Privacy Law, 3: 67-73. 2013.
Notice and Consent in a World of Big Data [link]Website   link   bibtex  
Face-to-Data--Another Developing Privacy Threat?. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law. 2013.
link   bibtex  
Data protection principles for the 21st century. Cate, F., H.; Cullen, P.; and Mayer-Schonberger, V. Microsoft Corporaton, 2013.
link   bibtex  
Year 1 Report: Center for Trustworthy Scientific Cyberinfrastructure. Welch, V. Technical Report Indiana University, 10 2013.
Year 1 Report: Center for Trustworthy Scientific Cyberinfrastructure [link]Website   link   bibtex   abstract  
Status, Strategies and Future Plans-OSG PKI Transition. Welch, V. Technical Report 2013.
link   bibtex  
Identity management factors for HEP virtual organizations. Cowles, R.; Jackson, C.; and Welch, V. In 20th International Conference on Computing in High Energy and Nuclear Physics (CHEP2013), 2013.
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XSEDE-enabled high-throughput lesion activity assessment. Zhang, H.; Boyles, M., J.; Ruan, G.; Li, H.; Shen, H.; and Ando, M. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13, pages 1, 2013.
XSEDE-enabled high-throughput lesion activity assessment [link]Website   doi   link   bibtex  
Discipline Categories (for Cyberinfrastructure) at Indiana University. Stewart, C., A. Technical Report 2013.
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Science gateway security recommendations. Basney, J.; and Welch, V. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, 2013.
Science gateway security recommendations [link]Website   doi   link   bibtex   abstract  
Identity Management for Virtual Organizations: An Experience-Based Model. Cowles, R.; Jackson, C.; and Welch, V. In 2013 IEEE 9th International Conference on e-Science, pages 278-284, 10 2013. IEEE
Identity Management for Virtual Organizations: An Experience-Based Model [link]Website   doi   link   bibtex   abstract  
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Haas, B., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P., Bowden, J., Couger, M., Eccles, D., Li, B., Lieber, M., MacManes, M., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C., Henschel, R., e., a.; Haas, B., J.; Papanicolaou, A.; Yassour, M.; Grabherr, M.; Blood, P., D.; Bowden, J.; Couger, M., B.; Eccles, D.; Li, B.; Lieber, M.; Macmanes, M., D.; Ott, M.; Orvis, J.; Pochet, N.; Strozzi, F.; Weeks, N.; Westerman, R.; William, T.; Dewey, C., N.; Henschel, R.; Leduc, R., D.; Friedman, N.; Regev, A.; and others Nature Protocols, 8(8): 1494-1512. 2013.
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis [link]Website   doi   link   bibtex   abstract  
Making campus bridging work for researchers: A case study with mlRho. Thota, A.; Michael, S.; Xu, S.; Haubold, B.; Doak, T.; and Henschel, R. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), pages 8, 2013.
Making campus bridging work for researchers: A case study with mlRho [link]Website   doi   link   bibtex   abstract  
XSEDE Cloud Survey Report. Lifka, David; Foster, Ian; Mehringer, Susan; Parashar, Manish; Redfern, Paul; Stewart, Craig; Tuecke, S. Technical Report 2013.
XSEDE Cloud Survey Report [pdf]Paper   XSEDE Cloud Survey Report [link]Website   link   bibtex   abstract  
Final report on accomplishments of a Task Force on Campus Bridging sponsored workshop: Campus Leadership Engagement in Building a Coherent Campus Cyberinfrastructure 2013 Citation: "Final report on accomplishments of a Task Force on Campus Bridging sponso. Dreher, P.; Ahalt, S., C.; Stewart, C., A.; Pepin, J., M.; Almes, G., T.; Mundrane, M.; Dreher, P.; Stewart, C., A.; Pepin, J., M.; Almes, G., T.; Mundrane, M.; and Ahalt, S., C. Technical Report 2013.
Final report on accomplishments of a Task Force on Campus Bridging sponsored workshop: Campus Leadership Engagement in Building a Coherent Campus Cyberinfrastructure 2013 Citation: "Final report on accomplishments of a Task Force on Campus Bridging sponso [link]Website   link   bibtex   abstract  
Report about the collaboration between UITS/Research Technologies at Indiana University and the Center for Information Services and High Performance Computing at Technische Universität Dresden, Germany (2011-2012). Henschel, R.; Stewart, C., A.; William, T.; Nagel, W.; Henschel, R.; Stewart, C., A.; William, T.; Müller, M.; and Nagel, W., ". Technical Report 2013.
Report about the collaboration between UITS/Research Technologies at Indiana University and the Center for Information Services and High Performance Computing at Technische Universität Dresden, Germany (2011-2012) [pdf]Paper   Report about the collaboration between UITS/Research Technologies at Indiana University and the Center for Information Services and High Performance Computing at Technische Universität Dresden, Germany (2011-2012) [link]Website   link   bibtex   abstract  
  2012 (142)
Cognitive architectures: A way forward for the psychology of programming. Hansen, M., E.; Lumsdaine, A.; and Goldstone, R., L. In Proceedings of the ACM international symposium on New ideas, new paradigms, and reflections on programming and software, pages 27-38, 2012. ACM
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Breaking the speed and scalability barriers for graph exploration on distributed-memory machines. Checconi, F.; Petrini, F.; Willcock, J.; Lumsdaine, A.; Choudhury, A., R.; and Sabharwal, Y. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, pages 13, 2012. IEEE Computer Society Press
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The design and implementation of a multi-level content-addressable checkpoint file system. Kulkarni, A.; Manzanares, A.; Ionkov, L.; Lang, M.; and Lumsdaine, A. In High Performance Computing (HiPC), 2012 19th International Conference on, pages 1-10, 2012. IEEE
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Avalanche: a fine-grained flow graph model for irregular applications on distributed-memory systems. Willcock, J., J.; Newton, R., R.; and Lumsdaine, A. In Proceedings of the 1st ACM SIGPLAN workshop on Functional high-performance computing, pages 15-26, 2012. ACM
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Award ER25844: Minimizing System Noise Effects for Extreme-Scale Scientific Simulation Through Function Delegation. Lumsdaine, A. Technical Report 2012.
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Plenoptic rendering with interactive performance using GPUs. Lumsdaine, A.; Chunev, G.; and Georgiev, T. In Proceedings of SPIE - The International Society for Optical Engineering, volume 8295, 2012.
Plenoptic rendering with interactive performance using GPUs [link]Website   doi   link   bibtex   abstract  
GoDEL: A multidirectional dataflow execution model for large-scale computing. Kulkarni, A.; Lang, M.; and Lumsdaine, A. In Proceedings - 2011 1st Workshop on Data-Flow Execution Models for Extreme Scale Computing, DFM 2011, pages 10-18, 2012.
GoDEL: A multidirectional dataflow execution model for large-scale computing [link]Website   doi   link   bibtex   abstract  
Declarative parallel programming for GPUs. Holk, E.; Byrd, W.; Mahajan, N.; Willcock, J.; Chauhan, A.; and Lumsdaine, A. Advances in Parallel Computing, 22: 297-304. 2012.
Declarative parallel programming for GPUs [link]Website   doi   link   bibtex   abstract  
Optimizing latency and throughput for spawning processes on massively multicore processors. Lumsdaine, A., K., A.; Ionkov, M., L., L.; Kulkarni, A.; Lumsdaine, A., K., A.; Lang, M.; and Ionkov, L. In Proceedings of the 2nd International Workshop on Runtime and Operating Systems for Supercomputers, ROSS 2012 - In Conjunction with: ICS 2012, 2012.
Optimizing latency and throughput for spawning processes on massively multicore processors [link]Website   doi   link   bibtex   abstract  
Toward a core undergraduate curriculum in parallel and distributed computing. Prasad, S., K.; Gupta, A.; Kant, K.; Lumsdaine, A.; Padua, D.; Robert, Y.; Rosenberg, A.; Sussman, A.; and Weems, C. Computer Education, (2012-6). 2012.
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Position Paper: Logic Programming for Parallel Irregular Applications. Willcock, J., J.; and Lumsdaine, A. In High Performance Computing, Networking, Storage and Analysis (SCC), 2012 SC Companion:, pages 269-272, 2012. IEEE
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Towards a new execution model for HPC clouds. Sterling, T.; and Anderson, M. In Proceedings of Science, 2012.
Towards a new execution model for HPC clouds [link]Website   link   bibtex   abstract  
Compiled MPI: Cost-Effective Exascale Applications Development. Bronevetsky, G.; Quinlan, D.; Lumsdaine, A.; and Hoefler, T. Technical Report 2012.
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Guest editor's introduction: Special section on challenges and solutions in multicore and many-core computing. Zhou, S.; Qiu, J.; and Hawick, K. Concurrency Computation Practice and Experience, 24(1). 2012.
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FutureGrid education: Using case studies to develop a curriculum for communicating parallel and distributed computing concepts. Mitchell, J.; Qiu, J.; Canonio, M.; Jha, S.; Hayden, L.; O'Leary, B.; Figueiredo, R.; and Fox, G., C. In ACM International Conference Proceeding Series, 2012.
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Using Cloud Computing for Scalable, Reproducible Experimentation. Klinginsmith, J.; and Qiu, J. In ACM Symposium on Cloud Computing 2012, 2012. August
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Accelerating data transfers in iterative MapReduce framework. Zhang, B.; and Qiu, J. Indiana University, USA. 2012.
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High performance multidimensional scaling for large high-dimensional data visualization. Bae, S.; Qiu, J.; and Fox, G., C. IEEE Transaction of Parallel and Distributed System. 2012.
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Editorial for Emerging Computational Methods for the Life Sciences Workshop Special Issue 2012. Qiu, J.; Foster, I.; and Goble, C. Concurrency and Computation: Practice and Experience, 26(6). 2012.
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FutureGrid education: using case studies to develop a curriculum for communicating parallel and distributed computing concepts. Mitchell, J., E.; Qiu, J.; Canonio, M.; Jha, S.; Hayden, L.; O'Leary, B., A.; Figueiredo, R.; and Fox, G., C. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond, pages 61, 2012. ACM
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Recursive thinkers and doers in CS1. Cottam, J., A.; and Menzel, S. In Proceedings of the 43rd ACM technical symposium on Computer Science Education, pages 669, 2012. ACM
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Adaptive interpolation of multidimensional scaling. Bae, S., S.; Qiu, J.; and Fox, G., C. Procedia Computer Science, 9: 393-402. 2012.
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Hymr: a hybrid mapreduce workflow system. Ruan, Y.; Guo, Z.; Zhou, Y.; Qiu, J.; and Fox, G., C. In Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences, pages 39-48, 2012. ACM
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DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequences. Ruan, Y.; Ekanayake, S.; Rho, M.; Tang, H.; Bae, S., S.; Qiu, J.; and Fox, G., C. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pages 329-336, 2012. ACM
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Mining hidden mixture context with adios-p to improve predictive pre-fetcher accuracy. Choi, J., Y., J.; Abbasi, H.; Pugmire, D.; Podhorszki, N.; Klasky, S.; Capdevila, C.; Parashar, M.; Wolf, M.; Qiu, J.; and Fox, G., C. In E-Science (e-Science), 2012 IEEE 8th International Conference on, pages 1-8, 2012. IEEE
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Cinet: A cyberinfrastructure for network science. Abdelhamid, S., E.; Alo, R.; Arifuzzaman, S., M.; Beckman, P.; Bhuiyan, M., H.; Bisset, K.; Fox, E., E., A.; Fox, G., C., G.; Hall, K.; Hasan, S., M., S.; Joshi, A.; Khan, M.; Kuhlman, C.; Lee, S.; Leidig, J.; Makkapati, H.; Marathe, M.; Mortveit, H.; Qiu, J.; Ravi, S.; Shams, Z.; Sirisaengtaksin, O.; Subbiah, R.; Swarup, S.; Trebon, N.; Vullikanti, A.; and Zhao, Z. In E-Science (e-Science), 2012 IEEE 8th International Conference on, pages 1-8, 2012. IEEE
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Performance model for parallel matrix multiplication with dryad: Dataflow graph runtime. Li, H.; Fox, G., C.; and Qiu, J. In Cloud and Green Computing (CGC), 2012 Second International Conference on, pages 675-683, 2012. IEEE
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Performance of windows multicore systems on threading and mpi. Qiu, J.; and Bae, S., S. Concurrency and Computation: Practice and Experience, 24(1): 14-28. 2012.
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MiniKanren, live and untagged: Quine generation via relational interpreters (programming pearl). Byrd, W., E.; Holk, E.; and Friedman, D., P. In Proceedings of the ACM SIGPLAN International Conference on Functional Programming, ICFP, pages 8-29, 2012. Association for Computing Machinery
MiniKanren, live and untagged: Quine generation via relational interpreters (programming pearl) [link]Website   doi   link   bibtex   abstract  
Spatial autocorrelation-based information visualization evaluation. Cottam, J., A.; and Lumsdaine, A. In Proceedings of the 2012 BELIV Workshop: Beyond Time and Errors-Novel Evaluation Methods for Visualization, pages 8, 2012. ACM
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Improving the scalability of parallel N-body applications with an event-driven constraint-based execution model. Dekate, C.; Anderson, M.; Brodowicz, M.; Kaiser, H.; Adelstein-Lelbach, B.; and Sterling, T. International Journal of High Performance Computing Applications, 26(3): 319-332. 2012.
Improving the scalability of parallel N-body applications with an event-driven constraint-based execution model [link]Website   doi   link   bibtex   abstract  
Efficient dynamic data visualization with persistent data structures. Cottam, J., A.; and Lumsdaine, A. In Proceedings of SPIE - The International Society for Optical Engineering, volume 8294, pages 82940X, 2012.
Efficient dynamic data visualization with persistent data structures [link]Website   doi   link   bibtex   abstract  
Watch this: A taxonomy for dynamic data visualization. Cottam, J., A.; Lumsdaine, A.; and Weaver, C. In Visual Analytics Science and Technology (VAST), 2012 IEEE Conference on, pages 193-202, 2012. IEEE
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Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. Hughes, A.; Ruan, Y.; Ekanayake, S.; Bae, S., S.; Dong, Q.; Rho, M.; Qiu, J.; and Fox, G., C. BMC bioinformatics, 13(2): S9. 2012.
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Using Clouds for Technical Computing. Fox, G., C.; and Gannon, D. In High Performance Computing Workshop (1), pages 81-102, 2012.
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Programming Paradigms for Technical Computing on Clouds and Supercomputers. Fox, G., C.; and Gannon, D. In Proc. of the Cloud Futures Workshop, Berkley, California, 2012.
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Mobile interface design for low-literacy populations. Chaudry, B., M.; Connelly, K., H.; Siek, K., A.; and Welch, J., L. In Proceedings of the 2nd ACM SIGHIT international health informatics symposium, pages 91-100, 2012. ACM
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Toward total quality of experience: A QoE model in a communication ecosystem. Laghari, K., U., R.; and Connelly, K. IEEE Communications Magazine, 50(4). 2012.
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Risk communication design for older adults. Garg, V.; Camp, L., J.; Lorenzen-Huber, L., M.; and Connelly, K. ISG* ISARC. 2012.
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Best intentions: health monitoring technology and children. Toscos, T.; Connelly, K.; and Rogers, Y. In Proceedings of the SIGCHI conference on Human Factors in Computing Systems, pages 1431-1440, 2012. ACM
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Risk communication design: Video vs. text. Garg, V.; Camp, L., J.; Connelly, K.; and Lorenzen-Huber, L. In International Symposium on Privacy Enhancing Technologies Symposium, pages 279-298, 2012. Springer
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Aging, privacy, and home-based computing: Developing a design framework. Shankar, K.; Camp, L., J.; Connelly, K.; and Huber, L. IEEE Pervasive Computing, 11(4): 46-54. 2012.
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Opportunities for ubiquitous computing in the homes of low SES older adults. White, G., E.; Connelly, K., H.; and Caine, K., E. In Proceedings of the 2012 ACM Conference on Ubiquitous Computing, pages 659-660, 2012. ACM
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An offline mobile nutrition monitoring intervention for varying-literacy patients receiving hemodialysis: a pilot study examining usage and usability. Connelly, K.; Siek, K., A.; Chaudry, B.; Jones, J.; Astroth, K.; and Welch, J., L. Journal of the American Medical Informatics Association, 19(5): 705-712. 2012.
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Text messages for encouraging physical activity Are they effective after the novelty effect wears off?. Mutsuddi, A., U.; and Connelly, K. In Pervasive Computing Technologies for Healthcare (PervasiveHealth), 2012 6th International Conference on, pages 33-40, 2012. IEEE
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Cloud programming paradigms for technical computing applications. Fox, G., C.; and Gannon, D. In Proc. Cloud Futures Workshop, 2012.
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A Concept Design for the STL. Stroustrup, B.; Sutton, A.; Voufo, L.; and Zalewski, M. ISO/IEC JTC1/SC22/WG21 document N, 3351. 2012.
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Testing C++ generic libraries. Sutton, A.; and Zalewski, M. In Software Maintenance (ICSM), 2012 28th IEEE International Conference on, pages 36-45, 2012. IEEE
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Enabling hierarchical dissemination of streams in content distribution networks. Pallickara, S.; and Fox, G., C. Concurrency and Computation: Practice and Experience, 24(14): 1594-1606. 2012.
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Special issue for data intensive eScience. Qiu, J.; and Gannon, D. Distributed and Parallel Databases, 30(5-6): 303-306. 10 2012.
Special issue for data intensive eScience [link]Website   doi   link   bibtex   abstract  
ParamChem force field parametrization engine: Initial guess generation and dihedral parameter optimization. Vanommeslaeghe, K.; Shen, N.; Polani, N., K.; Fan, Y.; Ghosh, J.; Herath, C.; Marru, S.; Pierce, M.; Pamidighantam, S., V.; Sheetz, M.; and others In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 244, 2012.
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Building Scientific Workflows for the Geosciences with Open Community Software. Pierce, M., E.; Marru, S.; and Weerawarana, S., M. In AGU Fall Meeting Abstracts, 2012.
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Simplex GPS and InSAR Inversion Software. Donnellan, A.; Parker, J., W.; Lyzenga, G., A.; and Pierce, M., E. Technical Report 2012.
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Designing a road map for geoscience workflows. Duffy, C.; Gil, Y.; Deelman, E.; Marru, S.; Pierce, M.; Demir, I.; and Wiener, G. Eos, Transactions American Geophysical Union, 93(24): 225-226. 2012.
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Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools. Brookes, E.; Singh, R.; Pierce, M.; Marru, S.; Demeler, B.; and Rocco, M. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond, pages 42, 2012.
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A Workflows Roadmap for the Geosciences. Gil, Y.; Deelman, E.; Demir, I.; Duffy, C.; Marru, S.; Altintas, I.; Pierce, M., E.; Wiener, G.; Braeckel, A.; Browdy, S., F.; and others Technical Report 2012.
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Web service andworkflow abstractions to large scale nuclear physics calculations. Herath, C.; Liu, F.; Marru, S.; Gunathilake, L.; Sosonkina, M.; Vary, J., P.; Maris, P.; and Pierce, M. In Services Computing (SCC), 2012 IEEE Ninth International Conference on, pages 703-710, 2012.
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Designing a Roadmap for Workflow Cyberinfrastructure in the Geosciences: From Big Data to the Long Tail. Gil, Y.; Deelman, E.; Demir, I.; Duffy, C.; Marru, S.; Pierce, M., E.; and Wiener, G. In AGU Fall Meeting Abstracts, 2012.
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A high throughput workflow environment for cosmological simulations. Brandon, E.; Evrard, A., E.; Singh, R.; Marru, S.; Pierce, M.; Becker, M., R.; Kravtsov, A., V.; Busha, M., T.; Wechsler, R., H.; and Ricker, P., M. In American Astronomical Society Meeting Abstracts# 221, volume 221, pages 34, 2012.
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VOLUNTEER REVIEWERS. Abdelrahman, T., S.; Abramson, D.; Anderson, E.; Bartlett, R.; Becla, J.; Bernreuther, M.; Budavari, T.; Cagnoni, S.; Calvayrac, F.; Camelli, F.; and others Computing in Science & Engineering, 14: 87. 2012.
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Genomics, Transcriptomics, and Proteomics: Engaging Biologists (Workshop). LeDuc, R., D. In eScience 2012, 2012.
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What is campus bridging and what is XSEDE doing about it?. Stewart, C., A.; Bachmann, F.; Hazlewood, V.; Knepper, R.; Foster, I.; Ferguson, J.; Grimshaw, A.; and Lifka, D. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12, pages 1, 2012. ACM Press
What is campus bridging and what is XSEDE doing about it? [link]Website   doi   link   bibtex   abstract  
A common path forward for the immersive visualization community. Wernert, E., A.; Sherman, W., R.; O'Leary, P.; and Whiting, E. Technical Report 2012.
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A large scale evolutionary analysis of the internet autonomous system network. Stewart, C.; and Khan, J. In Proceedings of the 9th International Conference on Information Technology, ITNG 2012, 2012.
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Open Science Grid (OSG) ticket synchronization: Keeping your home field advantage in a distributed environment. Gross, K.; Hayashi, S.; Teige, S.; and Quick, R. Journal of Physics: Conference Series, 396(PART 6). 2012.
Open Science Grid (OSG) ticket synchronization: Keeping your home field advantage in a distributed environment [link]Website   doi   link   bibtex   abstract  
Technical Report: Report on Lustre use across an experimental 100Gb network spanning 2,175 mi. Henschel, R.; Simms, S., C.; Hancock, D., Y.; Michael, S.; Johnson, T.; Heald, N.; William, T.; Berry, D.; Allen, M.; and Knepper, R. Technical Report 2012.
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The event notification and alarm system for the Open Science Grid operations center. Hayashi, S.; Teige, S.; and Quick, R. Journal of Physics: Conference Series, 396(PART 3). 2012.
The event notification and alarm system for the Open Science Grid operations center [link]Website   doi   link   bibtex   abstract  
SPEC OMP2012 - An application benchmark suite for parallel systems using OpenMP. Müller, M., S.; Baron, J.; Brantley, W., C.; Feng, H.; Hackenberg, D.; Henschel, R.; Jost, G.; Molka, D.; Parrott, C.; Robichaux, J.; Shelepugin, P.; Van Waveren, M.; Whitney, B.; and Kumaran, K. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7312 LNCS: 223-236. 2012.
SPEC OMP2012 - An application benchmark suite for parallel systems using OpenMP [link]Website   doi   link   bibtex   abstract  
The IQ-wall and IQ-station--harnessing our collective intelligence to realize the potential of ultra-resolution and immersive visualization. Wernert, E., A.; Sherman, W., R.; Eller, C.; Reagan, D.; Beard, P., D.; Whiting, E., T.; and O'Leary, P. Technical Report 2012.
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Xsede campus bridging use cases. Stewart, C., A.; Knepper, R.; Grimshaw, A.; Foster, I.; Bachmann, F.; Lifka, D.; Riedel, M.; and Tueke, S. Technical Report 2012.
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Reordering virtual reality: Recording and recreating real-time experiences. Dolinsky, M.; Sherman, W.; Wernert, E.; and Chi, Y., C. In Proceedings of SPIE - The International Society for Optical Engineering, volume 8289, 2012. SPIE
Reordering virtual reality: Recording and recreating real-time experiences [link]Website   doi   link   bibtex   abstract  
Campus Bridging Use Case Quality Attribute Scenarios. Stewart, C., A.; Knepper, R.; Grimshaw, A.; Foster, I.; Bachmann, F.; Lifka, D.; Riedel, M.; and Tuecke, S. Technical Report 2012.
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Study of nuclear decays during a solar eclipse: Thule Greenland 2008. Javorsek II, D.; Brewer, M.; Buncher, J.; Fischbach, E.; Gruenwald, J.; Heim, J.; Hoft, A.; Horan, T.; Kerford, J.; Kohler, M.; Lau, J.; Longman, A.; Mattes, J.; Mohsinally, T.; Newport, J.; Petrelli, M.; Stewart, C.; Jenkins, J.; Lee, R.; Morreale, B.; Morris, D.; Mudry, R.; O'Keefe, D.; Terry, B.; Silver, M.; and Sturrock, P. Astrophysics and Space Science, 342(1). 2012.
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Using stereoscopic 3D videos to inform the public about the benefits of computational science. Boyles, M., J.; Frend, C.; William, A., M.; and Eller, C. In ACM International Conference Proceeding Series, 2012.
Using stereoscopic 3D videos to inform the public about the benefits of computational science [link]Website   doi   link   bibtex   abstract  
Demonstrating Lustre over a 100Gbps wide area network of 3,500km. Henschel, R.; Simms, S.; Hancock, D.; Michael, S.; Johnson, T.; Heald, N.; William, T.; Berry, D.; Allen, M.; Knepper, R.; Davy, M.; Link, M.; and Stewart, C., A. In 2012 International Conference for High Performance Computing, Networking, Storage and Analysis, of SC '12, pages 1-8, 11 2012. IEEE
Demonstrating Lustre over a 100Gbps wide area network of 3,500km [link]Website   doi   link   bibtex   abstract   1 download  
The benefits and challenges of sharing glidein factory operations across nine time zones between OSG and CMS. Sfiligoi, I.; Dost, J., M.; Zvada, M.; Butenas, I.; Holzman, B.; Wuerthwein, F.; Kreuzer, P.; Teige, S., W.; Quick, R.; Hernández, J., M.; and Flix, J. Journal of Physics: Conference Series, 396(PART 3). 2012.
The benefits and challenges of sharing glidein factory operations across nine time zones between OSG and CMS [link]Website   doi   link   bibtex   abstract  
Temporal representation for scientific data provenance. Chen, P.; Plale, B.; and Aktas, M. In 2012 IEEE 8th International Conference on E-Science, e-Science 2012, 2012.
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SEAD Virtual Archive: Building a Federation of Institutional Repositories for Long Term Data Preservation. Plale, B.; McDonald, R., H.; Chandrasekar, K.; Kouper, I.; Konkiel, S.; Hedstrom, M., L.; Myers, J.; and Kumar, P. International Journal of Digital Curation, 8(2). 2012.
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Exploiting network parallelism for improving data transfer performance. Gunter, D.; Kettimuthu, R.; Kissel, E.; Swany, M.; Yi, J.; and Zurawski, J. In Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012, 2012.
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Visualizing large scale scientific data provenance. Chen, P.; and Plale, B. In Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012, 2012.
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Effectiveness of hybrid workflow systems for computational science. Plale, B.; Withana, E.; Herath, C.; Chandrasekar, K.; and Luo, Y. In Procedia Computer Science, volume 9, 2012.
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Efficient data transfer protocols for big data. Tierney, B.; Kissel, E.; Swany, M.; and Pouyoul, E. In 2012 IEEE 8th International Conference on E-Science, e-Science 2012, 2012.
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Hierarchical MapReduce programming model and scheduling algorithms. Luo, Y.; and Plale, B. In Proceedings - 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, CCGrid 2012, 2012.
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Managing the long tail of science: Data and communities. Plale, B. In ACM International Conference Proceeding Series, 2012.
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Validating linux network emulation. Kissel, E.; and Swany, M. Technical Report 2012.
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Middleware alternatives for storm surge predictions in Windows Azure. Chandrasekar, K.; Pathirage, M.; Wijeratne, S.; Mattocks, C.; and Plale, B. In ScienceCloud '12 - 3rd Workshop on Scientific Cloud Computing, 2012.
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Provenance analysis: Towards quality provenance. Cheah, Y.; and Plale, B. In 2012 IEEE 8th International Conference on E-Science, e-Science 2012, 2012.
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Temporal Data Mining of Scientific Data Provenance. Chen, P.; Plale, B.; and Aktas, M. Technical Report 2012.
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The extensible session protocol: A protocol for future internet architectures. Kissel, E.; and Swany, M. Rapport technique. 2012.
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Driving software defined networks with XSP. Kissel, E.; Fernandes, G.; Jaffee, M.; Swany, M.; and Zhang, M. In IEEE International Conference on Communications, 2012.
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Opening Data in the Long Tail for Community Discovery, Curation and Action Using Active and Social Curation. Hedstrom, M., L.; Kumar, P.; Myers, J.; and Plale, B., A. In AGU Fall Meeting Abstracts, 2012.
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Pipelined parallel LZSS for streaming data compression on GPGPUs. Ozsoy, A.; Swany, M.; and Chauhan, A. In Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS, 2012.
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Second International Workshop on Traceability and Compliance of Semi-Structured Processes (TC4SP 2011). Curbera, F.; Leymann, F.; Nezhad, H.; and Plale, B. Volume 99 LNBIP 2012.
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Qualitative Comparison of Multiple Cloud Frameworks. Von Laszewski, G.; Diaz, J.; Wang, F.; and Fox, G., G., C. In Proceedings: 2012 IEEE 5th international conference on cloud computing, pages 734-741, 2012.
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Design of an accounting and metric-based cloud-shifting and cloud-seeding framework for federated clouds and bare-metal environments. Von Laszewski, G.; Lee, H.; Diaz, J.; Wang, F.; Tanaka, K.; Karavinkoppa, S.; Fox, G., C., G.; and Furlani, T. In FederatedClouds'12 - Proceedings of the 2012 Workshop on Cloud Services, Federation, and the 8th Open Cirrus Summit, Co-located with ICAC'12, 2012.
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Supporting experimental computer science. Desprez, F.; Fox, G., C.; Jeannot, E.; Keahey, K.; Kozuch, M.; Margery, D.; Neyron, P.; Nussbaum, L.; Perez, C.; and Richard, O. INRIA, 2012.
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Design of a Dynamic Provisioning System for a Federated Cloud and Bare-metal Environment. von Laszewski, G.; Lee, H.; Diaz, J.; Wang, F.; Tanaka, K.; Karavinkoppa, S.; Fox, G., C.; and Furlani, T. In Proc. Workshop on Cloud Services, Federation, and the 8th Open Cirrus Summit, 2012.
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Data analytics driven cyberinfrastructure operations, planning and analysis using XDMoD. Furlani, T., R.; Schneider, B., I.; Jones, M., D.; Towns, J.; Hart, D., L.; Patra, A., K.; DeLeon, R., L.; Gallo, S., M.; Lu, C.; and Ghadersohi, A. In submitted SC12 Conference, Salt Lake City, Utah, 2012.
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Abstract image management and universal image registration for cloud and HPC infrastructures. Diaz, J.; Von Laszewski, G.; Wang, F.; and Fox, G., C. In Proceedings - 2012 IEEE 5th International Conference on Cloud Computing, CLOUD 2012, 2012.
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Message from the program co-chairs. Von Laszewski, G.; Grossman, R.; Milojicic, D.; Kozuch, M.; and McGeer, R. In FederatedClouds'12 - Proceedings of the 2012 Workshop on Cloud Services, Federation, and the 8th Open Cirrus Summit, Co-located with ICAC'12, 2012.
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Scalable integrated performance analysis of multi-gigabit networks. Kissel, E.; El-Hassany, A.; Fernandes, G.; Swany, M.; Gunter, D.; Samak, T.; and Schopf, J. In Proceedings of the 2012 IEEE Network Operations and Management Symposium, NOMS 2012, 2012.
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Mining classifications from social-ecological databases. Jensen, S.; Chen, M.; Liu, X.; Plale, B.; and Leake, D. Proceedings of the ASIST Annual Meeting, 49(1). 2012.
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Generalized representation and mapping for social-ecological data: Freeing data from the database. Jensen, S.; Plale, B.; Liu, X.; Chen, M.; Leake, D.; and England, J. In 2012 IEEE 8th International Conference on E-Science, e-Science 2012, 2012.
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From metadata to ontology representation: A case of converting severe weather forecast metadata to an ontology. Chen, M.; and Plale, B. In Proceedings of the ASIST Annual Meeting, volume 49, 2012.
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Evaluating high performance data transfer with RDMA-based protocols in wide-area networks. Kissel, E.; and Swany, M. In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012, 2012.
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Sigiri: Uniform resource abstraction for grids and clouds. Withana, E.; and Plale, B. Concurrency Computation Practice and Experience, 24(18). 2012.
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The challenges and opportunities of workflow systems in environmental research. Plale, B. In WIRADA Science Symposium Proceedings, Melbourne, Australia, August, pages 1-5, 2012.
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Visualization of network data provenance. Chen, P.; Plale, B.; Cheah, Y.; Ghoshal, D.; Jensen, S.; and Luo, Y. In 19th International Conference on High Performance Computing, HiPC 2012, 2012.
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HathiTrust Research Center: Computational Research on the HathiTrust Repository. Plale, B., A.; Poole, M., S.; McDonald, R., H.; and Unsworth, J. Technical Report Indiana University, 2012.
HathiTrust Research Center: Computational Research on the HathiTrust Repository [link]Website   link   bibtex  
Active and Social Data Curation: Reinventing the Business of Community-scale Lifecycle Data Management. McDonald, R., H.; Kumar, P.; Plale, B., A.; Myers, J., D.; and Hedstrom, M., L. In AGU Fall Meeting Abstracts, 2012.
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E-DECIDER: experience developing earthquake disaster decision support and response tools. Glasscoe, M.; Donnellan, A.; Stough, T.; Parker, J.; Burl, M.; Granat, R.; Pierce, M.; Wang, J.; Ma, Y.; Rundle, J.; and others In 9th US-Japan Natural Resources Panel on Earthquake Research, 2012. Pasadena, CA: Jet Propulsion Laboratory, National Aeronautics and Space Administration, 2012.
E-DECIDER: experience developing earthquake disaster decision support and response tools [link]Website   link   bibtex  
QuakeSim Project Networking. Kong, D.; Donnellan, A.; and Pierce, M., E. In AGU Fall Meeting Abstracts, 2012.
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QuakeSim 2.0. Donnellan, A.; Parker, J., W.; Lyzenga, G., A.; Granat, R., A.; Norton, C., D.; Rundle, J., B.; Pierce, M., E.; Fox, G., C.; McLeod, D.; and Ludwig, L., G. Technical Report 2012.
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Using UAVSAR to Estimate Creep Along the Superstition Hills Fault, Southern California. Donnellan, A.; Parker, J., W.; Pierce, M.; and Wang, J. In AGU Fall Meeting Abstracts, 2012.
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Web service and workflow abstractions to large scale nuclear physics calculations. Herath, C.; Liu, F.; Marru, S.; Gunathilake, L.; Sosonkina, M.; Vary, J., P.; Maris, P.; and Pierce, M. In Proceedings - 2012 IEEE 9th International Conference on Services Computing, SCC 2012, pages 703-710, 2012.
Web service and workflow abstractions to large scale nuclear physics calculations [link]Website   doi   link   bibtex   abstract  
Using service-based GIS to support earthquake research and disaster response. Wang, J.; Pierce, M.; Ma, Y.; Fox, G., C.; Donnellan, A.; Parker, J.; and Glasscoe, M. Computing in Science & Engineering, 14(5): 21-30. 2012.
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QuakeSim: Integrated modeling and analysis of geologic and remotely sensed data. Donnellan, A.; Parker, J.; Granat, R.; De Jong, E.; Suzuki, S.; Pierce, M.; Fox, G., C.; Rundle, J.; McLeod, D.; Al-Ghanmi, R.; and others In Aerospace Conference, 2012 IEEE, pages 1-9, 2012.
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A distributed approach to computational earthquake science: Opportunities and challenges. Donnellan, A.; Parker, J.; Glasscoe, M.; De Jong, E.; Pierce, M.; Fox, G., C.; McLeod, D.; Rundle, J.; and Ludwig, L., G. Computing in Science & Engineering, 14(5): 31-42. 2012.
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Multiple Stream Transfer Support in NaradaBrokering. Lim, S., B.; Kapla, A.; Pallickara, S.; Pierce, M.; and Fox, G., C. Journal of Convergence Information Technology, 7(9). 2012.
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Globus Online Security Review. Welch, V. Technical Report 2012.
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The Supreme Court and information privacy. Cate, F., H.; and Cate, B., E. International Data Privacy Law, 2(4): 255-267. 2012.
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PRIVACY, CONSUMER CREDIT, AND THE. Cate, F., H. The Impact of Public Policy on Consumer Credit,229. 2012.
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The Intricacies of Independence. Cate, F., H.; Kuner, C.; Millard, C.; and Svantession, D., J., B. International Data Privacy Law, 2(1): 1-2. 2012.
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Security at the Cyber Border: Exploring Cybersecurity for International Research Network Connections. Welch, V.; Pearson, D.; Tierney, B.; and Williams, J. Technical Report 2012.
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OSG Certificate Authority Implementation Plan. Welch, V. Technical Report 2012.
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The commodification of information and the control of expression. Cate, F., H. Amicus Curiae, 2002(43): 3-7. 2012.
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The End of the Beginning. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 2(3): 115-116. 2012.
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OSG DigiCert Pilot Report. Altunay, M.; Basney, J.; Fischer, J.; Sehgal, C.; and Welch, V. Technical Report 2012.
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A high throughput workflow environment for cosmological simulations. Erickson, B., M., S.; Singh, R.; Evrard, A., E.; Becker, M., R.; Busha, M., T.; Kravtsov, A., V.; Marru, S.; Pierce, M.; and Wechsler, R., H. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12, pages 1, 2012. ACM Press
A high throughput workflow environment for cosmological simulations [pdf]Paper   A high throughput workflow environment for cosmological simulations [link]Website   doi   link   bibtex   abstract  
Exploiting HPC resources for the 3D-time series analysis of caries lesion activity. Zhang, H.; Henschel, R.; Li, H.; Kohara, E., K.; Boyles, M., J.; and Ando, M. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (XSEDE '12), pages 8, 2012.
Exploiting HPC resources for the 3D-time series analysis of caries lesion activity [link]Website   doi   link   bibtex   abstract  
Conducting K-12 outreach to evoke early interest in IT, science, and advanced technology. Kallback-Rose, K.; Seiffert, K.; Antolovic, D.; Miller, T.; Ping, R.; and Stewart, C. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12, pages 1, 2012. ACM Press
Conducting K-12 outreach to evoke early interest in IT, science, and advanced technology [link]Website   doi   link   bibtex   abstract  
Distributed Monitoring Infrastructure for Worldwide LHC Computing Grid. Andrade, P.; Babik, M.; Bhatt, K.; Chand, P.; Collados, D.; Duggal, V.; Fuente, P.; Hayashi, S.; Imamagic, E.; Joshi, P.; Kalmady, R.; Karnani, U.; Kumar, V.; Lapka, W.; Quick, R.; Tarragon, J.; Teige, S.; and Triantafyllidis, C. Journal of Physics: Conference Series, 396(3): 032002. 12 2012.
Distributed Monitoring Infrastructure for Worldwide LHC Computing Grid [link]Website   doi   link   bibtex   abstract  
XSEDE12 panel: Security for science gateways and campus bridging. Basney, J.; Butler, R.; Fraser, D.; Marru, S.; and Stewart, C. In ACM International Conference Proceeding Series, 2012.
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2012 Annual Report on Training, Education, and Outreach Activities of the Indiana University Pervasive Technology Institute and affiliated organizations. Miller, T.; Ping, R., J.; Plale, B., A.; and Stewart, C., A., C., A. Technical Report Pervasive Technology Institute, Indiana University Bloomington, 2012.
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48 Month Program Report. McRobbie, M., A.; Wheeler, B., C.; Plale, B., A.; and Stewart, C., A. Technical Report 2012.
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Trinity RNA-Seq assembler performance optimization. Henschel, R.; Nista, P., M.; Lieber, M.; Haas, B., J.; Wu, L.; Leduc, R., D.; and Henschel, R., Lieber, M., Wu, L-S, Nista, P. M., Haas, B.J., and LeDuc, R. In ACM International Conference Proceeding Series, 2012.
Trinity RNA-Seq assembler performance optimization [link]Website   doi   link   bibtex   abstract  
2012 Annual Report - Advanced Biomedical Information Technology Core. Barnett, W., K.; Shankar, G.; Hancock, D., Y.; Allen, M.; Seiffert, K.; Boyles, M.; Rogers, J., L.; Wernert, E.; Link, M., R.; Stewart, C., A.; Barnett, W., K.; Shankar, G.; Hancock, D., Y.; Allen, M.; Seiffert, K.; Boyles, M.; Rogers, J., L.; Wernert, E.; Link, M., R.; and Stewart, C., A. Technical Report 2012.
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Declarative Parallel Programming for GPUs. Holk, E.; Byrd, W., E.; Mahajan, N.; Willcock, J.; Chauhan, A.; and Lumsdaine, A. In PARCO, pages 297-304, 2011.
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Kanor. Holk, E.; Byrd, W.; Willcock, J.; Hoefler, T.; Chauhan, A.; and Lumsdaine, A. Practical Aspects of Declarative Languages,190-204. 2011.
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8 Scalable Parallel Solution Techniques for Data-Intensive Problems in Distributed Memory. Edmonds, N.; and Lumsdaine, A. In Fifth SIAM Workshop on Combinatorial Scientific Computing, May 19–21, 2011, Darmstadt, Germany, pages 26, 2011.
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Extending transfer entropy improves identification of effective connectivity in a spiking cortical network model. Ito, S.; Hansen, M., E.; Heiland, R.; Lumsdaine, A.; Litke, A., M.; and Beggs, J., M. PLoS ONE, 6(11). 2011.
Extending transfer entropy improves identification of effective connectivity in a spiking cortical network model [link]Website   doi   link   bibtex   abstract  
Reasonable abstractions: Semantics for dynamic data visualization. Cottam, J., A.; and Lumsdaine, A. In VAST 2011 - IEEE Conference on Visual Analytics Science and Technology 2011, Proceedings, pages 269-270, 2011.
Reasonable abstractions: Semantics for dynamic data visualization [link]Website   doi   link   bibtex   abstract  
Active pebbles: Parallel programming for data-driven applications. Willcock, J., J.; Hoefler, T.; Edmonds, N., G.; and Lumsdaine, A. In Proceedings of the International Conference on Supercomputing, pages 235-244, 2011. ACM
Active pebbles: Parallel programming for data-driven applications [link]Website   doi   link   bibtex   abstract  
Communication optimization beyond MPI. Friedley, A.; and Lumsdaine, A. In IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum, pages 2018-2021, 2011. IEEE
Communication optimization beyond MPI [link]Website   doi   link   bibtex   abstract  
Active pebbles: A programming model for highly parallel fine-grained data-driven computations. Willcock, J., J.; Hoefler, T.; Edmonds, N., G.; and Lumsdaine, A. In ACM SIGPLAN Notices, volume 46, pages 305-306, 2011. ACM
Active pebbles: A programming model for highly parallel fine-grained data-driven computations [link]Website   doi   link   bibtex   abstract  
A language for generic programming in the large. Siek, J., G.; and Lumsdaine, A. Science of Computer Programming, 76(5): 423-465. 2011.
A language for generic programming in the large [link]Website   doi   link   bibtex   abstract  
Partial globalization of partitioned address spaces for zero-copy communication with shared memory. Jiao, F.; Mahajan, N.; Willcock, J.; Chauhan, A.; and Lumsdaine, A. In 18th International Conference on High Performance Computing, HiPC 2011, pages 1-10, 2011. IEEE
Partial globalization of partitioned address spaces for zero-copy communication with shared memory [link]Website   doi   link   bibtex   abstract  
Cloud technologies for bioinformatics applications. Ekanayake, J.; Gunarathne, T.; and Qiu, J. IEEE Transactions on parallel and distributed systems, 22(6): 998-1011. 2011.
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Cloud computing paradigms for pleasingly parallel biomedical applications. Gunarathne, T.; Wu, T.; Choi, J., Y.; Bae, S.; and Qiu, J. Concurrency and Computation: Practice and Experience, 23(17): 2338-2354. 2011.
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Finding complex biological relationships in recent PubMed articles using Bio-LDA. Wang, H.; Ding, Y.; Tang, J.; Dong, X.; He, B.; Qiu, J.; and Wild, D., J. PloS one, 6(3): e17243. 2011.
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Communication and data-intensive science in the beginning of the 21st century. Faris, J.; Kolker, E.; Szalay, A.; Bradlow, L.; Deelman, E.; Feng, W.; Qiu, J.; Russell, D.; Stewart, E.; and Kolker, E. Omics: a journal of integrative biology, 15(4): 213-215. 2011.
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Experimenting lucene index on HBase in an HPC environment. Gao, X.; Nachankar, V.; and Qiu, J. In Proceedings of the first annual workshop on High performance computing meets databases, pages 25-28, 2011. ACM
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Portable parallel programming on cloud and hpc: Scientific applications of twister4azure. Gunarathne, T.; Zhang, B.; Wu, T.; and Qiu, J. In Utility and Cloud Computing (UCC), 2011 Fourth IEEE International Conference on, pages 97-104, 2011. IEEE
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Co-processing SPMD Computation on GPUs and CPUs on Shared Memory System. Li, H.; Fox, G., C.; Laszewski, G.; Guo, Z.; and Qiu, J. Technical Report 2011.
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Generalizing mapreduce as a unified cloud and HPC runtime. Qiu, J. In Proceedings of the 2nd international workshop on Petascal data analytics: challenges and opportunities, pages 37-38, 2011. ACM
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Design Pattern for Typical Scientific Applications in DryadLINQ CTP. Li, H.; Ruan, Y.; Zhou, Y.; Qiu, J.; and Fox, G., C. In DataCloud-SC '11 Proceedings of the second international workshop on Data intensive computing in the clouds, pages 61-70, 2011.
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Browsing large‐scale cheminformatics data with dimension reduction. Choi, J., Y.; Bae, S.; Qiu, J.; Chen, B.; and Wild, D. Concurrency and Computation: Practice and Experience, 23(17): 2315-2325. 2011.
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Iterative mapreduce for azure cloud. Gunarathne, T.; Qiu, J.; and Fox, G., C. CCA11 Cloud Computing and Its Applications, Chicago, ILL. 2011.
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Scalable programming and algorithms for data-intensive life science applications. Qiu, J. Omics: a journal of integrative biology, 15(4): 235-237. 2011.
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Scalable Parallel Scientific Computing Using Twister4Azure. Gunarathne, T.; Zhang, B.; Wu, T.; and Qiu, J. In UCC, 2011.
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Mining relational paths in integrated biomedical data. He, B.; Tang, J.; Ding, Y.; Wang, H.; Sun, Y.; Shin, J., H.; Chen, B.; Moorthy, G.; Qiu, J.; Desai, P.; Wild, D., J.; Desai, P.; Qiu, J.; Moorthy, G.; Chen, B.; Shin, J., H.; Sun, Y.; Wang, H.; Ding, Y.; and Tang, J. PLoS One, 6(12): e27506. 2011.
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Truthy: Mapping the spread of astroturf in microblog streams. Ratkiewicz, J.; Conover, M.; Meiss, M.; Gonçalves, B.; Patil, S.; Flammini, A.; and Menczer, F. In Proceedings of the 20th International Conference Companion on World Wide Web, WWW 2011, pages 249-252, 2011.
Truthy: Mapping the spread of astroturf in microblog streams [link]Website   doi   link   bibtex   abstract  
Properties and evolution of internet traffic networks from anonymized flow data. Meiss, M.; Menczer, F.; and Vespignani, A. ACM Transactions on Internet Technology, 10(4). 2011.
Properties and evolution of internet traffic networks from anonymized flow data [link]Website   doi   link   bibtex   abstract   1 download  
Privacy Framework for Older Adults. Garg, V.; Camp, L., J.; Connelly, K.; Shankar, K.; and Lorenzen-Huber, L., M. In Workshop on Security and Human Behavior, Pittsburgh, PA, 2011.
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Issues in evaluating ambient displays in the wild: two case studies. Hazlewood, W., R.; Stolterman, E.; and Connelly, K. In Proceedings of the SIGCHI conference on Human factors in computing systems, pages 877-886, 2011. ACM
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DigiSwitch: A device to allow older adults to monitor and direct the collection and transmission of health information collected at home. Caine, K., E.; Zimmerman, C., Y.; Schall-Zimmerman, Z.; Hazlewood, W., R.; Camp, L., J.; Connelly, K., H.; Huber, L., L.; and Shankar, K. Journal of medical systems, 35(5): 1181-1195. 2011.
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Designing risk communication for older adults. Garg, V.; Camp, L., J.; Mae, L.; and Connelly, K. In Symposium on Usable Privacy and Security (SOUPS), 2011.
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ScaleMirror: A pervasive device to aid weight analysis. Younge, A., J.; Periasamy, V.; Al-Azdee, M.; Hazlewood, W.; and Connelly, K. In CHI'11 Extended Abstracts on Human Factors in Computing Systems, pages 2335-2340, 2011. ACM
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" What's your number?": A survey of how parents and teens cope with diabetes in the context of technology support. Toscos, T.; Connelly, K.; and Rogers, Y. In Pervasive Computing Technologies for Healthcare (PervasiveHealth), 2011 5th International Conference on, pages 210-213, 2011. IEEE
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The design of a mobile portion size estimation interface for a low literacy population. Chaudry, B.; Connelly, K.; Siek, K., A.; and Welch, J., L. In Pervasive Computing Technologies for Healthcare (PervasiveHealth), 2011 5th International Conference on, pages 160-167, 2011. IEEE
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Performance evaluation of mapreduce applications on cloud computing environment, futuregrid. Kang, Y.; and Fox, G., C. Grid and Distributed Computing,77-86. 2011.
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ConceptClang: An implementation of C++ concepts in Clang. Voufo, L.; Zalewski, M.; and Lumsdaine, A. In WGP'11 - Proceedings of the 2011 ACM SIGPLAN Workshop on Generic Programming, pages 71-82, 2011. ACM
ConceptClang: An implementation of C++ concepts in Clang [link]Website   doi   link   bibtex   abstract  
The QuakeTables UAVSAR Repository-Delivering RPI Products to Geo-Science Applications. Al-Ghanmi, R.; McLeod, D.; Donnellan, A.; Parker, J., W.; Pierce, M.; and Zheng, Y. In AGU Fall Meeting Abstracts, 2011.
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Investigating the Use of Gadgets, Widgets, and OpenSocial to Build Science Gateways. Guo, Z.; Singh, R.; Pierce, M.; and Liu, Y. In E-Science (e-Science), 2011 IEEE 7th International Conference on, pages 31-38, 2011.
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Virtual laboratory for planetary materials (VLab): an updated overview of system service architecture. da Silveira, P., R., C.; Valdez, M., N.; Wenzcovitch, R., M.; Pierce, M.; da Silva, C., R., S.; and Yuen, D., A. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, pages 33, 2011.
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Transitioning BioVLab cloud workbench to a science gateway. Marru, S.; Chae, H.; Tangchaisin, P.; Kim, S.; Pierce, M.; and Nephew, K. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, pages 40, 2011.
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Apache airavata: a framework for distributed applications and computational workflows. Marru, S.; Gunathilake, L.; Herath, C.; Tangchaisin, P.; Pierce, M.; Mattmann, C.; Singh, R.; Gunarathne, T.; Chinthaka, E.; Gardler, R.; and others In Proceedings of the 2011 ACM workshop on Gateway computing environments, pages 21-28, 2011.
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UltraScan gateway enhancements: in collaboration with TeraGrid advanced user support. Demeler, B.; Singh, R.; Pierce, M.; Brookes, E., H.; Marru, S.; and Dubbs, B. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, pages 34, 2011.
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Open community development for science gateways with apache rave. Pierce, M., E.; Singh, R.; Guo, Z.; Marru, S.; Rattadilok, P.; and Goyal, A. In Proceedings of the 2011 ACM workshop on Gateway computing environments, pages 29-36, 2011.
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Statistical Analysis of GPS Timeseries from the Tohoku-Oki Earthquake at Multiple Time Resolutions. Granat, R., A.; Owen, S., E.; Moore, A., W.; Donnellan, A.; Gao, X.; Ma, Y.; and Pierce, M. In AGU Fall Meeting Abstracts, 2011.
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Campus Bridging Birds-of-a-Feather Session at TeraGrid 2011 Conference. Knepper, R.; and Stewart, C., A. Technical Report 2011.
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The shape of the TeraGrid: Analysis of TeraGrid users and projects as an affiliation network. Knepper, R. In Proceedings of the TeraGrid 2011 Conference: Extreme Digital Discovery, TG'11, 2011.
The shape of the TeraGrid: Analysis of TeraGrid users and projects as an affiliation network [link]Website   doi   link   bibtex   abstract  
Incorporating an advanced maintenance strategy improves equipment reliability and reduces cement plant costs. Conklin, C.; Stewart, C.; and Kurosky, J. In IEEE Cement Industry Technical Conference (Paper), 2011.
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Publications, presentations, and news pertaining to National Science Foundation grant number 0521433–MRI: Acquisition of a High-Speed, High Capacity Storage System to Support Scientific Computing: The Data Capacitor. Stewart, C., A.; and Simms, S., C. Technical Report 2011.
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Electronic poster: Performance studies of a molecular dynamics code. William, T.; Berry, D., K.; and Henschel, R. In SC'11 - Proceedings of the 2011 High Performance Computing Networking, Storage and Analysis Companion, Co-located with SC'11, pages 105-106, 2011.
Electronic poster: Performance studies of a molecular dynamics code [link]Website   doi   link   bibtex   abstract  
Economic development by the Indiana University Pervasive Technology Institute, Pervasive Technology Labs, and the Research Technologies Division of University Information Technology Services September 1999–June 2011: a public report. Stewart, C., A.; and Miller, T. Technical Report 2011.
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Technical Report: TeraGrid eXtreme Digital Campus Cyberinfrastructure and Campus Bridging Requirements Elicitation Meeting. Stewart, C., A.; McCaulay, D., S.; Jul, S.; and Moore, R., L. Technical Report 2011.
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GOC-TX: A reliable ticket synchronization application for the open science grid. Hayashi, S.; Gopu, A.; and Quick, R. Journal of Physics: Conference Series, 331(PART 8). 2011.
GOC-TX: A reliable ticket synchronization application for the open science grid [link]Website   doi   link   bibtex   abstract  
HMMerthread: Detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. Bradshaw, C., R.; Surendranath, V.; Henschel, R.; Mueller, M., S.; and Habermann, B., H. PLoS ONE, 6(3). 2011.
HMMerthread: Detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition [link]Website   doi   link   bibtex   abstract  
A Science Driven Production Cyberinfrastructure-the Open Science Grid. Altunay, M.; Avery, P.; Blackburn, K.; Bockelman, B.; Ernst, M.; Fraser, D.; Quick, R.; Gardner, R.; Goasguen, S.; Levshina, T.; Livny, M.; McGee, J.; Olson, D.; Pordes, R.; Potekhin, M.; Rana, A.; Roy, A.; Sehgal, C.; Sfiligoi, I.; and Wuerthwein, F. Journal of Grid Computing, 9(2): 201-218. 2011.
A Science Driven Production Cyberinfrastructure-the Open Science Grid [link]Website   doi   link   bibtex   abstract  
Technical Report: Survey of cyberinfrastructure needs and interests of NSF-funded principal investigators. Stewart, C., A.; Katz, D., S.; Hart, D., L.; Lantrip, D.; McCaulay, D., S.; and Moore, R., L. Technical Report 2011.
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Campus Bridging: Data and Networking Issues Workshop Report. Almes, G., T.; Jent, D.; and Stewart, C., A. Technical Report 2011.
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Atmospheric sciences and informatics EarthCube driver whitepaper: Technical infrastructure. Plale, B.; Clark, R.; Mattocks, C.; Brewster, K.; Barthelmie, R.; Droegemeier, K.; Gannon, D.; Graves, S.; Jensen, S.; and Mahoney, W. Technical Report 2011.
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A noisy 10GB provenance database. Cheah, Y., Y.; Plale, B.; Kendall-Morwick, J.; Leake, D.; and Ramakrishnan, L. In International Conference on Business Process Management, volume 100 LNBIP, pages 370-381, 2011. Springer
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Workflow Evolution: Tracing Workflows Through Time. Chinthaka, E.; Barga, R.; Plale, B.; and Araujo, N. Microsoft Research. 2011.
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A composite project effort estimation approach in an enterprise software development project. Catal, C.; and Aktas, M., S. In SEKE 2011 - Proceedings of the 23rd International Conference on Software Engineering and Knowledge Engineering, pages 331-334, 2011.
A composite project effort estimation approach in an enterprise software development project [link]Website   link   bibtex   abstract  
Using provenance for personalized quality ranking of scientific datasets. Simmhan, Y.; and Plale, B. International Journal of Computers and their Applications, 18(3). 2011.
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The Open Provenance Model core specification (v1.1). Moreau, L.; Clifford, B.; Freire, J.; Futrelle, J.; Gil, Y.; Groth, P.; Kwasnikowska, N.; Miles, S.; Missier, P.; Myers, J.; Plale, B.; Simmhan, Y.; Stephan, E.; and Den Bussche, J. Future Generation Computer Systems, 27(6). 2011.
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Understanding the effects of boundary layer and synoptic meteorology on new particle formation based on WRF simulations and measurements in Southern Indiana. Crippa, P.; El Afandi, G.; Plale, B.; and Pryor, S., C. In AGU Fall Meeting Abstracts, 2011.
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Strengths and weaknesses of sub-workflow interoperability. Plale, B.; Withana, E., C.; Herath, C.; Chandrasekar, K.; Luo, Y.; and Terkhorn, F. Technical Report 2011.
Strengths and weaknesses of sub-workflow interoperability [link]Website   link   bibtex  
Towards generic FutureGrid image management. Von Laszewski, G.; Diaz, J.; Wang, F.; Younge, A.; Kulshrestha, A.; and Fox, G., C. In Proceedings of the TeraGrid 2011 Conference: Extreme Digital Discovery, TG'11, 2011.
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FutureGrid image repository: A generic catalog and storage system for heterogeneous virtual machine images. Diaz, J.; Von Laszewski, G.; Wang, F.; Younge, A.; and Fox, G., C. In Proceedings - 2011 3rd IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2011, 2011.
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Threat detection in urban water distribution systems with simulations conducted in grids and clouds. Von Laszewski, G.; Wang, L.; Wang, F.; Fox, G., C., G.; and Mahinthakumar, G. Civil-Comp Proceedings, 95. 2011.
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FutureGrid User Support. Pike, G.; Younge, A.; von Laszewski, G.; Wang, F.; Diaz, J.; Kulshrestha, A.; and Fox, G., C. FutureGrid NSF Review, Indiana University. 2011.
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Task scheduling with ANN-based temperature prediction in a data center: a simulation-based study. Wang, L.; von Laszewski, G.; Huang, F.; Dayal, J.; Frulani, T.; and Fox, G., C. Engineering with Computers, 27(4): 381-391. 2011.
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Towards building a cloud for scientific applications. Wang, L.; Kunze, M.; Tao, J.; and von Laszewski, G. Advances in Engineering software, 42(9): 714-722. 2011.
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Towards cloud deployments using FutureGrid. von Laszewski, G.; Diaz, J.; Wang, F.; Fox, G., C.; von Laszewski, G.; Wang, F.; and Fox, G., C. Indiana University, Bloomington, IN, 47408. 2011.
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eMOLST: a documentation flow for distributed health informatics. von Laszewski, G.; Dayal, J.; and Wang, L. Concurrency and Computation: Practice and Experience, 23(16): 1857-1867. 2011.
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Towards on demand it service deployment. Dayal, J.; Rathbone, C.; Wang, L.; and von Laszewski, G. Internet Policies and Issues, 7: 249-262. 2011.
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WANG, Lizhe. Wang, L.; Kunze, M.; Tao, J.; Von Laszewski, G.; Chen, D.; Deng, Z.; Huang, F.; Khan, S., U.; Dayal, J.; and Chen, J. Advances in Engineering Software, 42(9): 714-722. 2011.
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Evaluation of Two XML Storage Approaches for Scientific Metadata. Jensen, S.; Ghoshal, D.; and Plale, B. Technical Report 2011.
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Sigiri: Uniform abstraction for large-scale compute resource interactions. Withana, E., C.; and Plale, B. School of Informatics and Computing, Indiana University, Bloomington, Indiana, Tech. Rep. TR693. 2011.
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Programming abstraction for resource aware stream processing for scientific workflows. Herath, C.; and Plale, B. In Proceedings - 7th IEEE International Conference on e-Science Workshops, eScienceW 2011, 2011.
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A hierarchical framework for cross-domain MapReduce execution. Luo, Y.; Guo, Z.; Sun, Y.; Plale, B.; Qiu, J.; and Li, W. In ECMLS'11 - Proceedings of the 2nd International Workshop on Emerging Computational Methods for the Life Sciences, 2011.
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Provenance Capture of Unmanaged Workflows with Karma. Plale, B.; Cao, B.; and Aktas, M. Bloomington, IN, Indiana University. 2011.
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Hybrid programming abstraction for e-science workflows and event processing. Herath, C.; and Plale, B. In DEBS'11 - Proceedings of the 5th ACM International Conference on Distributed Event-Based Systems, 2011.
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Data provenance for preservation of digital geoscience data. Plale, B.; Cao, B.; Herath, C.; and Sun, Y. Volume 482 2011.
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Key Provenance of Earth Science Observational Data Products. Aktas, M.; Plale, B.; Conover, H.; and Purohit, P. American Geophysical Union, (Fall Meeting 2011). 2011.
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Spatial Data in an Ontology for Research on Forest Resources. Jensen, S.; Cox, M.; Bender, D.; Chen, M.; England, J.; Plale, B.; and Leake, D. In COSIT'11 Workshop, pages 28-30, 2011.
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Escience workflows 9 years out: Converging on a vision. Plale, B.; Fox, G., C.; Kowalczyk, S.; and Chandrasekar, K. Technical Report 2011.
Escience workflows 9 years out: Converging on a vision [pdf]Website   link   bibtex  
QuakeSim: a Web Service Environment for Productive Investigations with Earth Surface Sensor Data. Parker, J., W.; Donnellan, A.; Granat, R., A.; Lyzenga, G., A.; Glasscoe, M., T.; McLeod, D.; Al-Ghanmi, R.; Pierce, M.; Fox, G., C.; Grant Ludwig, L.; and others In AGU Fall Meeting Abstracts, 2011.
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Automatic task re-organization in MapReduce. Guo, Z.; Pierce, M.; Fox, G., C.; and Zhou, M. In Cluster Computing (CLUSTER), 2011 IEEE International Conference on, pages 335-343, 2011.
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Distributed web security for science gateways. Basney, J.; Dooley, R.; Gaynor, J.; Marru, S.; and Pierce, M. In Proceedings of the 2011 ACM workshop on Gateway computing environments, pages 13-20, 2011.
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E-DECIDER: Earthquake Disaster Decision Support and Response Tools-Development and Experiences. Glasscoe, M., T.; Blom, R., G.; Bawden, G., W.; Fox, G., C.; Pierce, M.; Rundle, J., B.; Wang, J.; Ma, Y.; Sachs, M., K.; Parker, J., W.; and others In AGU Fall Meeting Abstracts, 2011.
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Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education. Guha, R.; Wiggins, G., D.; Wild, D., J.; Baik, M.; Fox, G., C.; and others In silico biology, 11(1, 2): 41-60. 2011.
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Privacy--An Elusive Concept. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 1(3). 2011.
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Campus Bridging: Software & Software Service Issues Workshop Report. McGee, J.; Welch, V.; and Almes, G., T. Technical Report 2011.
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Let's Not Kill All the Privacy Laws (and Lawyers). Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 1(4). 2011.
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Moving Forward Together. Cate, F., H.; Kuner, C.; Millard, C.; and Svantesson, D., J., B. International Data Privacy Law, 1(2): 81-82. 2011.
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An analysis of the benefits and risks to LIGO when participating in identity federations. Basney, J.; Koranda, S.; and Welch, V. LIGO document number LIGOG1100964v2, September. 2011.
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Overview of NSF ACCI Task Force on Campus Bridging Report. Stewart, C., A.; and Welch, V. Technical Report 2011.
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Report of NSF Workshop Series on Scientific Software Security Innovation Institute. Butler, R.; Welch, V.; Basney, J.; Koranda, S.; Barnett, W., K.; and Pearson, D. Technical Report 2011.
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A Transatlantic Convergence on Privacy?. Cate, F., H. IEEE Security & Privacy, 9(1): 76-79. 2011.
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Molecular parameter optimization gateway (ParamChem): Workflow management through TeraGrid ASTA. Ghosh, J.; Marru, S.; Singh, N.; Vanomesslaeghe, K.; Fan, Y.; and Pamidighantam, S. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery (TG '11), 2011.
Molecular parameter optimization gateway (ParamChem): Workflow management through TeraGrid ASTA [pdf]Paper   doi   link   bibtex   abstract  
Campus Bridging: Campus Leadership Engagement in Building a Coherent Campus Cyberinfrastructure Workshop Report. Dreher, P.; Ahalt, S.; Almes, G.; Mundrane, M.; Pepin, J.; and Stewart, C., A. Technical Report 2011.
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A Roadmap for Using NSF Cyberinfrastructure with InCommon: Abbreviated Version. Barnett, W.; Welch, V.; Walsh, A.; and Stewart, C., A. Technical Report 2011.
A Roadmap for Using NSF Cyberinfrastructure with InCommon: Abbreviated Version [link]Website   link   bibtex  
Cyberinfrastructure Usage Modalities on the TeraGrid. Katz, D., S.; Hart, D.; Jordan, C.; Majumdar, A.; Navarro, J.; Smith, W.; Towns, J.; Welch, V.; and Wilkins-Diehr, N. In Proceedings of the 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and PhD Forum (IPDPSW '11), pages 932-939, 5 2011. IEEE
Cyberinfrastructure Usage Modalities on the TeraGrid [link]Website   doi   link   bibtex   abstract  
Analysis of virtualization technologies for high performance computing environments. Younge, A., J.; Henschel, R.; Brown, J., T.; Von Laszewski, G.; Qiu, J.; and Fox, G., C. In Proceedings - 2011 IEEE 4th International Conference on Cloud Computing, CLOUD 2011, pages 9-16, 2011.
Analysis of virtualization technologies for high performance computing environments [link]Website   doi   link   bibtex   abstract  
A roadmap for using NSF cyberinfrastructure with InCommon. Welch, V.; Walsh, A.; Barnett, W.; Stewart, C., A.; Welch, V.; Walsh, A.; Stewart, C., A.; Barnett, W.; Stewart, C., A.; Welch, V.; Walsh, A.; and Stewart, C., A. In Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG '11, pages 1, 2011. ACM Press
A roadmap for using NSF cyberinfrastructure with InCommon [link]Website   doi   link   bibtex   abstract  
Indiana University's Advanced Cyberinfrastructure. Arenson, A.; Boyles, M.; Cruise, R.; Gopu, A.; Hart, D.; Lindenlaub, P.; Papakhian, M.; Samuel, J.; Seiffert, K.; and Shankar, A. Technical Report 2011.
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  2010 (90)
Hybrid cloud and cluster computing paradigms for life science applications. Qiu, J.; Ekanayake, J.; Gunarathne, T.; Choi, J., Y.; Bae, S.; Li, H.; Zhang, B.; Wu, T.; Ruan, Y.; and Ekanayake, S. In BMC bioinformatics, volume 11, pages S3, 2010. BioMed Central Ltd
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MapReduce in the Clouds for Science. Gunarathne, T.; Wu, T.; Qiu, J.; and Fox, G., C. In Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on, pages 565-572, 2010. IEEE
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Dimension reduction and visualization of large high-dimensional data via interpolation. Bae, S.; Choi, J., Y.; Qiu, J.; and Fox, G., C. In Proceedings of the 19th ACM international symposium on high performance distributed computing, pages 203-214, 2010. ACM
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Applying twister to scientific applications. Zhang, B.; Ruan, Y.; Wu, T.; Qiu, J.; Hughes, A.; and Fox, G., C. In Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on, pages 25-32, 2010. IEEE
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Twister: a runtime for iterative mapreduce. Ekanayake, J.; Li, H.; Zhang, B.; Gunarathne, T.; Bae, S.; Qiu, J.; and Fox, G., C. In Proceedings of the 19th ACM international symposium on high performance distributed computing, pages 810-818, 2010. ACM
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Multidimensional scaling by deterministic annealing with iterative majorization algorithm. Bae, S.; Qiu, J.; and Fox, G., C. In e-Science (e-Science), 2010 IEEE Sixth International Conference on, pages 222-229, 2010. IEEE
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An access control architecture for distributing trust in pervasive computing environments. Hill, R.; Al-Muhtadi, J.; and Byrd, W., E. In Proceedings - IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, EUC 2010, pages 695-702, 2010.
An access control architecture for distributing trust in pervasive computing environments [link]Website   doi   link   bibtex   abstract  
Map-reduce expansion of the ISGA genomic analysis web server. Hemmerich, C.; Hughes, A.; Ruan, Y.; Buechlein, A.; Qiu, J.; and Fox, G., C. IEEE CloudCom. 2010.
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Toward performance models of MPI implementations for understanding application scaling issues. Hoefler, T.; Gropp, W.; Thakur, R.; and Träff, J., L. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6305 LNCS: 21-30. 2010.
Toward performance models of MPI implementations for understanding application scaling issues [link]Website   doi   link   bibtex   abstract  
Software and hardware techniques for power-efficient HPC networking. Hoefler, T. Computing in Science and Engineering, 12(6): 30-37. 2010.
Software and hardware techniques for power-efficient HPC networking [link]Website   doi   link   bibtex   abstract  
AM++: A generalized active message framework. Willcock, J., J.; Hoefler, T.; Edmonds, N., G.; and Lumsdaine, A. In Parallel Architectures and Compilation Techniques - Conference Proceedings, PACT, pages 401-410, 2010.
AM++: A generalized active message framework [link]Website   doi   link   bibtex   abstract  
Efficient MPI support for advanced hybrid programming models. Hoefler, T.; Bronevetsky, G.; Barrett, B.; De Supinski, B., R.; and Lumsdaine, A. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6305 LNCS: 50-61. 2010.
Efficient MPI support for advanced hybrid programming models [link]Website   doi   link   bibtex   abstract  
Accurately measuring overhead, communication time and progression of blocking and nonblocking collective operations at massive scale. Hoefler, T.; Schneider, T.; and Lumsdaine, A. International Journal of Parallel, Emergent and Distributed Systems, 25(4): 241-258. 2010.
Accurately measuring overhead, communication time and progression of blocking and nonblocking collective operations at massive scale [link]Website   doi   link   bibtex   abstract  
Utilizing a social networking site as a web portal to process CReSIS radar data. Wood, J., A.; Hayden, L., B.; and Singh, R. In Proceedings of the 2010 TeraGrid Conference, TG '10, 2010.
Utilizing a social networking site as a web portal to process CReSIS radar data [link]Website   doi   link   bibtex   abstract  
Parallel zero-copy algorithms for Fast Fourier Transform and conjugate gradient using MPI datatypes. Hoefler, T.; and Gottlieb, S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6305 LNCS: 132-141. 2010.
Parallel zero-copy algorithms for Fast Fourier Transform and conjugate gradient using MPI datatypes [link]Website   doi   link   bibtex   abstract  
The PERCS high-performance interconnect. Arimilli, B.; Arimilli, R.; Chung, V.; Clark, S.; Denzel, W.; Drerup, B.; Hoefler, T.; Joyner, J.; Lewis, J.; Li, J.; Ni, N.; and Rajamony, R. In Proceedings - 18th IEEE Symposium on High Performance Interconnects, HOTI 2010, pages 75-82, 2010.
The PERCS high-performance interconnect [link]Website   doi   link   bibtex   abstract  
Radiolocation in ubiquitous wireless communication. Antolovic, D. Springer US, 2010.
Radiolocation in ubiquitous wireless communication [link]Website   doi   link   bibtex   abstract  
Agents, bookmarks and clicks: A topical model of Web navigation. Meiss, M., R.; Gonçalves, B.; Ramasco, J., J.; Flammini, A.; and Menczer, F. In HT'10 - Proceedings of the 21st ACM Conference on Hypertext and Hypermedia, pages 229-233, 2010.
Agents, bookmarks and clicks: A topical model of Web navigation [link]Website   doi   link   bibtex   abstract  
Modeling traffic on the web graph. Meiss, M., R.; Gonçalves, B.; Ramasco, J., J.; Flammini, A.; and Menczer, F. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6516 LNCS: 50-61. 2010.
Modeling traffic on the web graph [link]Website   doi   link   bibtex   abstract  
The Grid, Cloud Computing and our Manycore Future. Gannon, D. Technical Report 2010.
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Scalable communication protocols for dynamic sparse data exchange. Hoefler, T.; Siebert, C.; and Lumsdaine, A. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, volume 45, pages 159-168, 2010.
Scalable communication protocols for dynamic sparse data exchange [link]Website   doi   link   bibtex   abstract  
Enhancing learning: a study of how mobile devices can facilitate sensemaking. Rogers, Y.; Connelly, K.; Hazlewood, W.; and Tedesco, L. Personal and Ubiquitous Computing, 14(2): 111-124. 2010.
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Merging health literacy with computer technology: Self-managing diet and fluid intake among adult hemodialysis patients. Welch, J., L.; Siek, K., A.; Connelly, K., H.; Astroth, K., S.; McManus, M., S.; Scott, L.; Heo, S.; and Kraus, M., A. Patient education and counseling, 79(2): 192-198. 2010.
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DigiSwitch: design and evaluation of a device for older adults to preserve privacy while monitoring health at home. Caine, K., E.; Zimmerman, C., Y.; Schall-Zimmerman, Z.; Hazlewood, W., R.; Sulgrove, A., C.; Camp, L., J.; Connelly, K., H.; Huber, L., L.; and Shankar, K. In Proceedings of the 1st ACM international health informatics symposium, pages 153-162, 2010. ACM
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Journal of Management: Upcoming Issues. Aguinis, H.; Dalton, D., R.; Bosco, F., A.; Connelly, B.; Ireland, R., D.; Trevis, S.; Maertz Jr, C., P.; Boyar, S., L.; Combs, J., G.; and Ketchen Jr, D., J. Journal of Management, 36(6): 1608-1610. 2010.
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Ethics and Pervasive Technologies: A Collaborative Approach to Teaching. Shankar, K.; and Connelly, K., H. Teaching Ethics, 11(1): 75-85. 2010.
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Cultivating curious and creative minds: The role of teachers and teacher educators. Digby, A., D.; Alexander, G.; Basile, C., G.; Cloninger, K.; Connelly, F., M.; DeCuir-Gunby, J., T.; Gaa, J., P.; Ginsburg, H., P.; Haynes, A., M.; and He, M., F. R&L Education, 2010.
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Detecting and tracking the spread of astroturf memes in microblog streams. Ratkiewicz, J.; Conover, M.; Meiss, M.; Gonçalves, B.; Patil, S.; Flammini, A.; and Menczer, F. arXiv preprint arXiv:1011.3768. 2010.
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Generic programming with c++ concepts and haskell type classes—a comparison. Bernardy, J.; Jansson, P.; Zalewski, M.; and Schupp, S. Journal of Functional Programming, 20(3-4): 271-302. 2010.
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Restoring trust relationships within the framework of collaborative digital preservation federations. McDonald, R., H.; and Walters, T., O. Journal of Digital Information. 2010.
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QuakeTables: A Federated Ontology-Based Database System for Geoscience. Al-Ghanmi, R.; McLeod, D.; Grant Ludwig, L.; Donnellan, A.; Parker, J., W.; and Pierce, M. In AGU Fall Meeting Abstracts, 2010.
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The QuakeSim System for GPS Time Series Analysis. Granat, R., A.; Gao, X.; Pierce, M.; and Wang, J. In AGU Fall Meeting Abstracts, 2010.
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SS11-7 Cytokine expression profiles characteristic of immune imbalances in persistent post infectious fatigue. Katz, B., Z.; Fletcher, M., A.; Smith, F., A.; Taylor, R.; Vernon, S., D.; and Broderick, G. Cytokine, 52(1): 81. 2010.
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Integrating chemistry scholarship with web architectures, grid computing and semantic web. Challa, S., K.; Pierce, M.; and Marru, S. In Gateway Computing Environments Workshop (GCE), 2010, pages 1-8, 2010.
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Leveraging Pre-Existing Resources at Institutions of Higher Education for K-12 STEM Engagement. Boyles, M.; Frend, C.; Rogers, J.; William, A.; Reagan, D.; and Wernert, E. In EdMedia: World Conference on Educational Media and Technology, pages 143-151, 2010. Association for the Advancement of Computing in Education (AACE)
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A revolutionary new paradigm for the reduction and analysis of astronomical images. Michael, S.; Knezek, P.; Stobie, E.; Henschel, R.; and Simms, S. In Proceedings - 2010 6th IEEE International Conference on e-Science, eScience 2010, pages 168-175, 2010.
A revolutionary new paradigm for the reduction and analysis of astronomical images [link]Website   doi   link   bibtex   abstract  
Cyberinfrastructure Software Sustainability and Reusability: Report from an NSF-funded workshop. Stewart, C., A.; Almes, G., T.; and Wheeler, B., C. Technical Report 2010.
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A distributed workflow for an astrophysical OpenMP application: Using the data capacitor over WAN to enhance productivity. Henschel, R.; Michael, S.; and Simms, S. In HPDC 2010 - Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, pages 644-650, 2010.
A distributed workflow for an astrophysical OpenMP application: Using the data capacitor over WAN to enhance productivity [link]Website   doi   link   bibtex   abstract  
Implementation of a shared data repository and common data dictionary for fetal alcohol spectrum disorders research. Arenson, A., D.; Bakhireva, L., N.; Chambers, C., D.; Deximo, C., A.; Foroud, T.; Jacobson, J., L.; Jacobson, S., W.; Jones, K., L.; Mattson, S., N.; May, P., A.; Moore, E., S.; Ogle, K.; Riley, E., P.; Robinson, L., K.; Rogers, J.; Streissguth, A., P.; Tavares, M., C.; Urbanski, J.; Yezerets, Y.; Surya, R.; Stewart, C., A.; and Barnett, W., K. Alcohol, 44(7-8): 643-647. 11 2010.
Implementation of a shared data repository and common data dictionary for fetal alcohol spectrum disorders research [link]Website   doi   link   bibtex   abstract  
Systems survey of endocytosis by multiparametric image analysis. Collinet, C.; Stöter, M.; Bradshaw, C., R.; Samusik, N.; Rink, J., C.; Kenski, D.; Habermann, B.; Buchholz, F.; Henschel, R.; Mueller, M., S.; Nagel, W., E.; Fava, E.; Kalaidzidis, Y.; and Zerial, M. Nature, 464(7286): 243-249. 2010.
Systems survey of endocytosis by multiparametric image analysis [link]Website   doi   link   bibtex   abstract  
Preliminary results from nuclear decay experiments performed during the solar eclipse of August 1, 2008. Javorsek II, D.; Kerford, J.; Stewart, C.; Buncher, J.; Fischbach, E.; Gruenwald, J.; Heim, J.; Hoft, A.; Horan, T.; Jenkins, J.; Kohler, M.; Lee, R.; Longman, A.; Mattes, J.; Mohsinally, T.; Morreale, B.; Morris, D.; Mudry, R.; Newport, J.; O'Keefe, D.; Petrelli, M.; Silver, M.; Sturrock, P.; Terry, B.; and Willenberg, H. In AIP Conference Proceedings, volume 1265, 2010.
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Power spectrum analyses of nuclear decay rates. Javorsek, D.; Sturrock, P.; Lasenby, R.; Lasenby, A.; Buncher, J.; Fischbach, E.; Gruenwald, J.; Hoft, A.; Horan, T.; Jenkins, J.; Kerford, J.; Lee, R.; Longman, A.; Mattes, J.; Morreale, B.; Morris, D.; Mudry, R.; Newport, J.; O'Keefe, D.; Petrelli, M.; Silver, M.; Stewart, C.; and Terry, B. Astroparticle Physics, 34(3). 2010.
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IQ-station: A low cost portable immersive environment. Sherman, W., R.; O'Leary, P.; Whiting, E., T.; Grover, S.; and Wernert, E., A. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 6454 LNCS(PART 2): 361-372. 2010.
IQ-station: A low cost portable immersive environment [link]Website   doi   link   bibtex   abstract  
WORKEM: Representing and emulating distributed scientific workflow execution state. Ramakrishnan, L.; Gannon, D.; and Plale, B. In CCGrid 2010 - 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing, 2010.
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The LEAD gateway II: a hardened, persistent community resource for meteorological research and education. Plale, B.; Droegemeier, K., K.; and Mattocks, C. In 26th conference on interactive information and processing systems, 2010.
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A multi-dimensional classification model for scientific workflow characteristics. Ramakrishnan, L.; and Plale, B. In Proceedings of the ACM SIGMOD International Conference on Management of Data, 2010.
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Towards proxy workflow execution in environmental research: Application to vortex2. Plale, B.; Herath, C.; and Withana, E., C. In Environmental Research Workshop, 2010.
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Versioning for workflow evolution. Withana, E.; Plale, B.; Barga, R.; and Araujo, N. In HPDC 2010 - Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, 2010.
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BlogMiner: Web blog mining application for classification of movie reviews. Baloglu, A.; and Aktas, M., S. In 5th International Conference on Internet and Web Applications and Services, ICIW 2010, pages 77-84, 2010.
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Provide virtual distributed environments for grid computing on demand. Wang, L.; Von Laszewski, G.; Kunze, M.; Tao, J.; and Dayal, J. Advances in Engineering Software, 41(2): 213-219. 2010.
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Design of the Futuregrid experiment management framework. Von Laszewski, G.; Fox, G., C., G.; Wang, F.; Younge, A.; Kulshrestha, A.; Pike, G.; Smithy, W.; Vöcklerz, J.; Figueiredox, R.; Fortesx, J.; and Keahey, K. In 2010 Gateway Computing Environments Workshop, GCE 2010, 2010.
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Towards energy aware scheduling for precedence constrained parallel tasks in a cluster with DVFS. Wang, L.; Von Laszewski, G.; Dayal, J.; and Wang, F. In CCGrid 2010 - 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing, 2010.
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Provide virtual machine information for grid computing. Wang, L.; Von Laszewski, G.; Chen, D.; Tao, J.; and Kunze, M. IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans, 40(6): 1362-1374. 2010.
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Enabling energy-efficient analysis of massive neural signals using GPGPU. Chen, D.; Wang, L.; Wang, S.; Xiong, M.; von Laszewski, G.; and Li, X. In Green Computing and Communications (GreenCom), 2010 IEEE/ACM Int'l Conference on & Int'l Conference on Cyber, Physical and Social Computing (CPSCom), pages 147-154, 2010. IEEE
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Multicores in Cloud Computing: Research Challenges for Applications. Wang, L.; Tao, J.; von Laszewski, G.; and Marten, H. JCP, 5(6): 958-964. 2010.
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Cyberaide onServe: Software as a Service on Production Grids. Kurze, T.; Wang, L.; von Laszewski, G.; Tao, J.; Kunze, M.; Kramer, D.; and Karl, W. In Parallel Processing (ICPP), 2010 39th International Conference on, pages 395-403, 2010. IEEE
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Efficient resource management for cloud computing environments. Younge, A., J.; Von Laszewski, G.; Wang, L.; Lopez-Alarcon, S.; and Carithers, W. In Green Computing Conference, 2010 International, pages 357-364, 2010. IEEE
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Cyberaide virtual applicance: On-demand deploying middleware for cyberinfrastructure. Kurze, T.; Wang, L.; Von Laszewski, G.; Tao, J.; Kunze, M.; Wang, F.; Kramer, D.; Karl, W.; and Ekanayake, J. Volume 34 LNICST 2010.
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Schedule distributed virtual machines in a service oriented environment. Wang, L.; Von Laszewski, G.; Kunze, M.; and Tao, J. In Advanced Information Networking and Applications (AINA), 2010 24th IEEE International Conference on, pages 230-236, 2010. IEEE
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Virtual data system on distributed virtual machines in computational grids. Wang, L.; Laszewski, G., V.; Tao, J.; and Kunze, M. International Journal of Ad Hoc and Ubiquitous Computing, 6(4): 194-204. 2010.
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GreenIT service level agreements. von Laszewski, G.; and Wang, L. Grids and Service-Oriented Architectures for Service Level Agreements, pages 77-88. Springer, 2010.
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Power aware scheduling for parallel tasks via task clustering. Wang, L.; Tao, J.; von Laszewski, G.; and Chen, D. In Parallel and Distributed Systems (ICPADS), 2010 IEEE 16th International Conference on, pages 629-634, 2010. IEEE
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Schedule Virtual Machines in a Distributed Service Oriented Environment. Wang, L.; von Laszewski, G.; Kunze, M.; Tao, J.; Dayal, J.; and Rathbone, C. In 24th IEEE International Conference on Advanced Information Networking and Applications, pages 230-236, 2010. Eggenstein-Leopoldshafen, Germany
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Framing the issues of cloud computing & sustainability: A design perspective. Pan, Y.; Maini, S.; and Blevis, E. In Proceedings - 2nd IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2010, pages 603-608, 2010.
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Karma2: Provenance management for data-driven workflows. Simmhan, Y., L.; Plale, B.; and Gannon, D. Web Services Research for Emerging Applications: Discoveries and Trends: Discoveries and Trends, 317. 2010.
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Trading consistency for scalability in scientific metadata. Jensen, S.; and Plale, B. In Proceedings - 2010 6th IEEE International Conference on e-Science, eScience 2010, 2010.
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Usage patterns to provision for scientific experimentation in clouds. Withana, E.; and Plale, B. In Proceedings - 2nd IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2010, 2010.
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Application of Management Frameworks: A Case Study on Managing Workflow related Systems. Perera, S.; Marru, S.; Gunarathne, T.; Gannon, D.; and Plale, B. In Web Services, 2009. ICWS 2009. IEEE International Conference on, pages 519-526, 2010. IEEE
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Streamflow - Programming model for data streaming in scientific workflows. Herath, C.; and Plale, B. In CCGrid 2010 - 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing, 2010.
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Mobile web service architecture using context-store. Oh, S.; Aktas, M.; and Fox, G., C. KSII Transactions on Internet and Information Systems, 4(5): 836-858. 2010.
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QuakeSim Computational Infrastructure for Integrating DESDynI and UAVSAR Data into Earthquake Models. Donnellan, A.; Rundle, J., B.; Grant Ludwig, L.; McLeod, D.; Pierce, M.; Fox, G., C.; Al-Ghanmi, R., A.; Parker, J., W.; Granat, R., A.; Lyzenga, G., A.; and others In AGU Fall Meeting Abstracts, 2010.
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Advances in cheminformatics methodologies and infrastructure to support the data mining of large, heterogeneous chemical datasets. Guha, R.; Gilbert, K.; Fox, G., C.; Pierce, M.; Wild, D.; and Yuan, H. Current computer-aided drug design, 6(1): 50-67. 2010.
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Building a distributed block storage system for cloud infrastructure. Gao, X.; Ma, Y.; Pierce, M.; Lowe, M.; and Fox, G., C. In Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on, pages 312-318, 2010.
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Scientific data management in the cloud: A survey of technologies, approaches and challenges. Pallickara, S., L., S.; Pallickara, S., L., S.; and Pierce, M. Handbook of Cloud Computing, pages 517-533. Springer US, 2010.
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Cloud Computing for Geosciences. Fox, G., C.; and Pierce, M., E. Technical Report 2010.
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Science gateways: Harnessing clouds and software services for science. Wilkins-Diehr, N.; Baru, C.; Gannon, D.; Keahey, K.; McGee, J.; Pierce, M.; Wolski, R.; and Wu, W. Cloud Computing and Software Services,17. 2010.
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Open grid computing environments: advanced gateway support activities. Pierce, M.; Marru, S.; Singh, R.; Kulshrestha, A.; and Muthuraman, K. In Proceedings of the 2010 TeraGrid Conference, pages 16, 2010.
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Generative topographic mapping by deterministic annealing. Choi, J., Y.; Qiu, J.; Pierce, M.; and Fox, G., C. Procedia Computer Science, 1(1): 47-56. 2010.
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The Quakesim portal and services: new approaches to science gateway development techniques. Pierce, M., E.; Gao, X.; Pallickara, S., L.; Guo, Z.; and Fox, G., C. Concurrency and Computation: Practice and Experience, 22(12): 1732-1749. 2010.
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The limits of notice and choice. Cate, F., H. IEEE Security & Privacy, 8(2). 2010.
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Workflows for parameter studies of multi-cell modeling. Heiland, R.; Swat, M.; Zaitlen, B.; Glazier, J.; and Lumsdaine, A. In Proceedings of the 2010 Spring Simulation Multiconference on - SpringSim '10, pages 1, 2010. ACM Press
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Protecting privacy in health research: the limits of individual choice. Cate, F., H. California Law Review,1765-1803. 2010.
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Enabling Lustre WAN for production use on the TeraGrid: a lightweight UID mapping scheme. Walgenbach, J.; Simms, S., C.; Westneat, K.; and Miller, J., P. In Proceedings of the 2010 TeraGrid Conference, pages 19, 2010. ACM
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A Federated Approach to Information Management in Grids. Aktas, M., S.; Fox, G., C.; and Pierce, M. Volume 7 . Web Service Composition and New Frameworks in Designing Semantics: Innovations, pages 66-99. IGI Global, 2010.
Web Service Composition and New Frameworks in Designing Semantics: Innovations [link]Website   doi   link   bibtex   abstract  
High-performance hybrid information service architecture. Aktas, M., S.; and Pierce, M. Concurrency and Computation: Practice and Experience, 22(15): 2095-2123. 2010.
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Science on the TeraGrid. Katz, D., S.; Callaghan, S.; Harkness, R.; Jha, S.; Kurowski, K.; Manos, S.; Pamidighantam, S.; Pierce, M.; Plale, B.; and Song, C. Computational Methods in Science and Technology, Special, (2010): 81-97. 2010.
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Progress Report on Implementation of Recommendations from the Indiana University Cyberinfrastructure Research Taskforce. Stewart, C., A. Technical Report 2010.
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MyOSG: A user-centric information resource for OSG infrastructure data sources. Gopu, A.; Hayashi, S.; and Quick, R. In Proceedings of the 5th Grid Computing Environments Workshop at Supercomputing 2009, GCE09, 2009.
MyOSG: A user-centric information resource for OSG infrastructure data sources [link]Website   doi   link   bibtex   abstract  
Applicability of DryadLINQ to Scientific Applications. Ekanayake, J.; Gunarathne, T.; Qiu, J.; Fox, G., C.; Beason, S.; Choi, J., Y.; Ruan, Y.; Bae, S.; and Li, H. Community Grids Laboratory, Indiana University. 2009.
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Multicell simulations of development and disease using the CompuCell3D simulation environment. Swat, M., H.; Hester, S., D.; Balter, A., I.; Heiland, R., W.; Zaitlen, B., L.; and Glazier, J., A. Systems Biology,361-428. 2009.
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Evaluating the jaccard-tanimoto index on multi-core architectures. Sachdeva, V.; Freimuth, D., M.; and Mueller, C. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5544 LNCS(PART 1): 944-953. 2009.
Evaluating the jaccard-tanimoto index on multi-core architectures [link]Website   doi   link   bibtex   abstract  
Power-aware, application-based performance study of modern commodity cluster interconnection networks. Hoefler, T.; Schneider, T.; and Lumsdaine, A. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium, 2009.
Power-aware, application-based performance study of modern commodity cluster interconnection networks [link]Website   doi   link   bibtex   abstract  
Towards efficient mapreduce using MPI. Hoefler, T.; Lumsdaine, A.; and Dongarra, J. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5759 LNCS: 240-249. 2009.
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The effect of network noise on large-scale collective communications. Hoefler, T.; Schneider, T.; and Lumsdaine, A. Parallel Processing Letters, 19(4): 573-593. 2009.
The effect of network noise on large-scale collective communications [link]Website   doi   link   bibtex   abstract  
Implementation and analysis of nonblocking collective operations on SCI networks. Kaiser, C.; Hoefler, T.; Bierbaum, B.; and Bemmerl, T. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium, 2009.
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Sparse collective operations for MPI. Hoefler, T.; and Träff, J., L. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium, 2009.
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Demand-driven execution of static directed acyclic graphs using task parallelism. Kambadur, P.; Gupta, A.; Hoefler, T.; and Lumsdaine, A. In 16th International Conference on High Performance Computing, HiPC 2009 - Proceedings, pages 284-293, 2009.
Demand-driven execution of static directed acyclic graphs using task parallelism [link]Website   doi   link   bibtex   abstract  
Optimized routing for large-scale InfiniBand networks. Hoefler, T.; Schneider, T.; and Lumsdaine, A. In Proceedings - Symposium on the High Performance Interconnects, Hot Interconnects, pages 103-111, 2009.
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Group operation assembly language - A flexible way to express collective communication. Hoefler, T.; Siebert, C.; and Lumsdaine, A. In Proceedings of the International Conference on Parallel Processing, pages 574-581, 2009.
Group operation assembly language - A flexible way to express collective communication [link]Website   doi   link   bibtex   abstract  
LogGP in theory and practice - An in-depth analysis of modern interconnection networks and benchmarking methods for collective operations. Hoefler, T.; Schneider, T.; and Lumsdaine, A. Simulation Modelling Practice and Theory, 17(9): 1511-1521. 2009.
LogGP in theory and practice - An in-depth analysis of modern interconnection networks and benchmarking methods for collective operations [link]Website   doi   link   bibtex   abstract  
The impact of network noise at large-scale communication performance. Hoefler, T.; Schneider, T.; and Lumsdaine, A. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium, 2009.
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Gene networks in Drosophila melanogaster: Integrating experimental data to predict gene function. Costello, J., C.; Dalkilic, M., M.; Beason, S., M.; Gehlhausen, J., R.; Patwardhan, R.; Middha, S.; Eads, B., D.; and Andrews, J., R. Genome Biology, 10(9). 2009.
Gene networks in Drosophila melanogaster: Integrating experimental data to predict gene function [link]Website   doi   link   bibtex   abstract  
Numerical investigation of algorithms for multi-antenna radiolocation. Antolovic, D. In IEEE Vehicular Technology Conference, 2009.
Numerical investigation of algorithms for multi-antenna radiolocation [link]Website   doi   link   bibtex   abstract  
What's in a session: Tracking individual behavior on the web. Meiss, M.; Duncan, J.; Gonçalves, B.; Ramasco, J., J.; and Menczer, F. In Proceedings of the 20th ACM Conference on Hypertext and Hypermedia, HT'09, pages 173-182, 2009.
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An algorithm for simultaneous radiolocation of multiple sources. Antolovic, D. In IEEE Vehicular Technology Conference, 2009.
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Project bloom: Empowering the security research community through data products and computing. Gupta, M.; Travis, G., R.; Ripley, D., A., J.; and Pearson, D., D. In 5th IEEE Workshop on Secure Network Protocols, NPSEC'09, pages 19-24, 2009.
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Enforcing user-defined management logic in large scale systems. Perera, S.; and Gannon, D. In Services-I, 2009 World Conference on, pages 243-250, 2009. IEEE
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A distributed framework for collaborative annotation of streams. Huang, T.; Pallickara, S.; and Fox, G., C. In Collaborative Technologies and Systems, 2009. CTS'09. International Symposium on, pages 440-447, 2009. IEEE
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Granules: A lightweight, streaming runtime for cloud computing with support, for map-reduce. Pallickara, S.; Ekanayake, J.; and Fox, G., C. In Cluster Computing and Workshops, 2009. CLUSTER'09. IEEE International Conference on, pages 1-10, 2009. IEEE
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Merging Literacy with Computer Technology for Self-Managing Diet and Fluid Intake. Welch, J., L.; Connelly, K.; Siek, K., A.; Jones, J.; Perkins, S., M.; Chaudry, B.; Kain, J.; Scott, L.; Astroth, K.; and Heo, S. Patient education and counseling. 2009.
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A Collaborative Approach to Minimize Cellphone Interruptions. Khalil, A.; and Connelly, K. Human-Computer Interaction–INTERACT 2009,874-877. 2009.
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Evaluation of two mobile nutrition tracking applications for chronically ill populations with low literacy skills. Siek, K., A.; Connelly, K., H.; Chaudry, B.; Lambert, D.; and Welch, J., L. Mobile Health Solutions for Biomedical Applications,1-23. 2009.
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Cloud technologies for bioinformatics applications. Qiu, X.; Ekanayake, J.; Beason, S.; Gunarathne, T.; Fox, G., C.; Barga, R.; and Gannon, D. In Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers, pages 6, 2009. ACM
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VGrADS: enabling e-Science workflows on grids and clouds with fault tolerance. Ramakrishnan, L.; Koelbel, C.; Kee, Y.; Wolski, R.; Nurmi, D.; Gannon, D.; Obertelli, G.; YarKhan, A.; Mandal, A.; and Huang, T., M. In High Performance Computing Networking, Storage and Analysis, Proceedings of the Conference on, pages 1-12, 2009. IEEE
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Workflows and e-Science: An overview of workflow system features and capabilities. Deelman, E.; Gannon, D.; Shields, M.; and Taylor, I. Future generation computer systems, 25(5): 528-540. 2009.
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A Semantic Definition of Separate Type Checking in C++ with Concepts. Zalewski, M.; and Schupp, S. Journal of Object Technology, 8(5): 105-132. 2009.
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Remembering what we like: Toward an agent-based model of Web traffic. Gonçalves, B.; Meiss, M., R.; Ramasco, J., J.; Flammini, A.; and Menczer, F. arXiv preprint arXiv:0901.3839. 2009.
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Granules: A Lightweight Runtime for Cloud Computing. Pallickara, S.; and Fox, G. Technical Report 2009.
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Efficiency Benefits in Mobile Web Service Architecture Using Context-store. Oh, S.; Aktas, M.; and Fox, G., C. Information Systems, 3(2): 1-21. 2009.
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Supporting cloud computing with the virtual block store system. Gao, X.; Lowe, M.; Ma, Y.; and Pierce, M. In E-Science Workshops, 2009 5th IEEE International Conference on, pages 71-78, 2009.
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Dynamic Resource-Critical Workflow Scheduling in Heterogeneous Environments. Gong, Y.; Pierce, M., E.; and Fox, G., C. In JSSPP, pages 1-15, 2009.
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The QuakeSim Web Portal Environment for GPS Data Analysis. Granat, R.; Gao, X.; and Pierce, M. 2009.
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Investigation of periodic nuclear decay data with spectral analysis techniques. Javorsek II, D.; Stunock, P.; Buncher, J.; Fischbach, E.; Gruenwald, T.; Hoft, A.; Horan, T.; Jenkins, J.; Kerford, J.; Lee, R.; Mattes, J.; Morris, D.; Mudry, R.; Newport, J.; Petrelli, M.; Silver, M.; Stewart, C.; Terry, B.; and Willenberg, H. In AIP Conference Proceedings, volume 1182, 2009.
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Network Workbench Tool. Vespignani, A.; Wasserman, S.; Wernert, E.; Huang, W., B.; Herr, B.; Zhang, H.; Balcan, D.; Hook, B.; Markines, B.; and Fortunato, S. Technical Report 2009.
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ID2–A Scalable and Flexible Mixed-Media Information Visualization System for Public Learning Exhibits. Wernert, E.; Lakshmipathy, J.; Boyles, M.; and Borner, K. In EdMedia: World Conference on Educational Media and Technology, pages 3848-3856, 2009. Association for the Advancement of Computing in Education (AACE)
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Virtual simulation for lighting and design education. Boyles, M.; Rogers, J.; Goreham, K.; Frank, M., A.; and Cowan, A., J. In Proceedings - IEEE Virtual Reality, pages 275-276, 2009.
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Acquisition of a High-Speed, High Capacity Storage System to Support Scientific Computing: The Data Capacitor Final Report. Stewart, C., A.; Simms, S., C.; Pilachowski, C.; and Bramley, R. Technical Report 2009.
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Where information searches for you: The visible past ubiquitous knowledge environment for digital humanities. Matei, S., A.; Wernert, E.; and Faas, T. In Proceedings - 12th IEEE International Conference on Computational Science and Engineering, CSE 2009, volume 4, pages 1043-1047, 2009.
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Virtual reality technology and the teaching of architectural lighting. Frank, M., A.; Cowan, D.; Boyles, M.; Rogers, J.; Goreham, K.; Suryabrata, J.; and Kodrat, Y. In ASEE Annual Conference and Exposition, Conference Proceedings, 2009. American Society for Engineering Education
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GeneIndex: An Open Source Parallel Program for Enumerating and Locating Words in a Genome. Li, H.; Hart, D.; Mueller, M.; Markwardt, U.; and Stewart, C. In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, pages 98-102, 2009. IEEE
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Developing a Coherent Cyberinfrastructure from Local Campuses to National Facilities: Challenges and Strategies. Stewart, C., A.; Pepin, J.; Odegard, J.; Hauser, T.; Fratkin, S.; Almes, G.; Ahalt, S.; Agarwala, V.; and Dreher, P. Technical Report 2009.
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MyOSG. Gopu, A.; Hayashi, S.; and Quick, R. In Proceedings of the 5th Grid Computing Environments Workshop on - GCE '09, pages 1, 2009. ACM Press
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Exploiting maximal redundancy to optimize SQL queries. Cao, B.; and Badia, A. Knowledge and Information Systems, 20(2): 187-220. 2009.
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Provenance information model of Karma version 3. Cao, B.; Plale, B.; Subramanian, G.; Robertson, E.; and Simmhan, Y. In SERVICES 2009 - 5th 2009 World Congress on Services, 2009.
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Principles and experiences: Designing and building enterprise information systems. Aktas, M., S. IGI Global, 2009.
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Karma2: Provenance management for data-driven workflows. Simmhan, Y.; Plale, B.; and Gannon, D. 2009.
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Cyberaide Virtual Applicance: On-Demand Deploying Middleware for Cyberinfrastructure. Kurze, T.; Wang, L.; Von Laszewski, G.; Tao, J.; Kunze, M.; Wang, F.; Kramer, D.; Karl, W.; and Ekanayake, J. In International Conference on Cloud Computing, pages 132-144, 2009. Springer
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Towards Thermal Aware Workload Scheduling in a Data Center. Wang, L.; Dayal, J.; and von Laszewski, G. In Pervasive Systems, Algorithms, and Networks (ISPAN), 2009 10th International Symposium on, 2009.
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Cyberaide creative: On-demand cyberinfrastructure provision in clouds. Rathbone, C.; Wang, L.; Von Laszewski, G.; and Wang, F. In I-SPAN 2009 - The 10th International Symposium on Pervasive Systems, Algorithms, and Networks, 2009.
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Thermal aware workload scheduling with backfilling for green data centers. Wang, L.; von Laszewski, G.; Dayal, J.; and Furlani, T., R. In Performance Computing and Communications Conference (IPCCC), 2009 IEEE 28th International, pages 289-296, 2009. IEEE
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Flexible framework for commodity FPGA cluster computing. Espenshade, J.; Lukowiak, M.; Shaaban, M.; and von Laszewski, G. In Field-Programmable Technology, 2009. FPT 2009. International Conference on, pages 465-471, 2009. IEEE
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Grid virtualization engine: design, implementation, and evaluation. Wang, L.; Von Laszewski, G.; Tao, J.; and Kunze, M. IEEE Systems Journal, 3(4): 477-488. 2009.
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Water Threat Management Report. von Laszewski, G. Technical Report 2009.
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Towards cyberinfrastructure for multi-scale crop disease early warning systems. Baker, K.; Plale, B.; Zaslavsky, I.; and Marru, S. In ASABE - 7th World Congress on Computers in Agriculture and Natural Resources 2009, WCCA 2009, 2009.
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CBR based workflow composition assistant. Chinthaka, E.; Ekanayake, J.; Leake, D.; and Plale, B. In 5th 2009 World Congress on Services, SERVICES 2009, 2009.
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Semantically annotated provenance in the Life Science Grid. Cao, B.; Plale, B.; Subramanian, G.; Missier, P.; Goble, C.; and Simmhan, Y. In SWPM'09 Proceedings of the First International Conference on Semantic Web in Provenance Management, volume 526, 2009.
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Application of management frameworks to manage workflow-based systems: A case study on a large scale e-science project. Perera, S.; Marru, S.; Gunarathne, T.; Gannon, D.; and Plale, B. In Web Services, 2009. ICWS 2009. IEEE International Conference on, pages 519-526, 2009. IEEE
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AVATS: Audio-video and textual synchronization. Maini, S.; Rosen, J.; Pierce, M., E.; and Fox, G., C. In Collaborative Technologies and Systems, 2009. CTS'09. International Symposium on, pages 455-464, 2009.
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QuakeSim: Increasing Utility of Spacebourne and Ground-based Earthquake Fault Data. Parker, J., W.; Glasscoe, M., T.; Donnellan, A.; Granat, R., A.; Rundle, J., B.; McLeod, D.; Al-Ganmi, R.; Grant Ludwig, L.; Fox, G., C.; Pierce, M.; and others In AGU Fall Meeting Abstracts, 2009.
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Unified Data Access/query over Integrated Data-views for Decision Making in Geographic Information Systems. Sayar, A.; Fox, G., C.; and Pierce, M., E. Grid Technology for Maximizing Collaborative Decision Management and Support: Advancing Effective Virtual Organizations: Advancing Effective Virtual Organizations,245. 2009.
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Cloud computing and spatial cyberinfrastructure. Pierce, M., E.; Fox, G., C.; Ma, Y.; and Wang, J. Journal of Computer Science of Indiana University,1-21. 2009.
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Grids challenged by a Web 2.0 and multicore sandwich. Fox, G., C.; and Pierce, M. Concurrency and Computation: Practice and Experience, 21(3): 265-280. 2009.
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Building the polargrid portal using web 2.0 and opensocial. Guo, Z.; Singh, R.; and Pierce, M. In Proceedings of the 5th Grid Computing Environments Workshop, pages 5, 2009.
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Enabling large scale scientific computations for expressed sequence tag sequencing over grid and cloud computing clusters. Pallickara, S., L.; Pierce, M.; Dong, Q.; and Kong, C. In PPAM 2009 EIGHTH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING AND APPLIED MATHEMATICS Wroclaw, Poland, 2009.
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BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome. Li, L.; Bum-Erdene, K.; Baenziger, P., H.; Rosen, J., J.; Hemmert, J., R.; Nellis, J., A.; Pierce, M., E.; and Meroueh, S., O. Nucleic acids research, 38(suppl_1): D765--D773. 2009.
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Using Web 2.0 for scientific applications and scientific communities. Pierce, M., E.; Fox, G., C.; Choi, J., Y.; Guo, Z.; Gao, X.; and Ma, Y. Concurrency and Computation: Practice and Experience, 21(5): 583-603. 2009.
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Web 2.0 for Grids and e-Science. Fox, G., C.; Guha, R.; McMullen, D., F.; Mustacoglu, A., F.; Pierce, M., E.; Topcu, A., E.; and Wild, D., J. Grid enabled remote instrumentation,409-431. 2009.
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Security, privacy, and the role of law. Cate, F., H. IEEE Security & Privacy, 7(5). 2009.
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Updating Data Protection: Part I--Identifying the Objectives. Cate, F., H. Published by the Centre for Information Policy Leadership. 2009.
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Dos and Don'ts of Data Breach and Information Security Policy. Cate, F., H.; Abrams, M., E.; Bruening, P., J.; and Swindle, O. Published by the Centre for Information Policy Leadership. 2009.
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Where information searches for you. Matei, S., A.; Wernert, E.; and Faas, T. In Computational Science and Engineering, 2009. CSE '09. International Conference on, 2009.
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Algorithms and the Grid. Fox, G., C.; Aktas, M., S.; Aydin, G.; Gadgil, H.; Pallickara, S.; Pierce, M., E.; and Sayar, A. Computing and visualization in science, 12(3): 115-124. 2009.
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Open grid computing environments. Pierce, M.; Marru, S.; Wu, W.; Kandaswami, G.; von Laszewski, G.; Dooley, R.; Dahan, M.; Wilkins-Diehr, N.; Thomas, M.; and Center, T. In Proceedings of the Fourth Annual TeraGrid Conference, 2009.
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  2008 (66)
α lean TA P: A declarative theorem prover for first-order classical logic. Near, J., P.; Byrd, W., E.; and Friedman, D., P. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5366 LNCS: 238-252. 2008.
α lean TA P: A declarative theorem prover for first-order classical logic [link]Website   doi   link   bibtex   abstract  
Multistage switches are not crossbars: Effects of static routing in high-performance networks. Hoefler, T.; Schneider, T.; and Lumsdaine, A. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, volume Proceeding, pages 116-125, 2008. Institute of Electrical and Electronics Engineers Inc.
Multistage switches are not crossbars: Effects of static routing in high-performance networks [link]Website   doi   link   bibtex   abstract  
Brief announcement: Leveraging non-blocking collective communication in high-performance applications. Hoefler, T.; Gottschling, P.; and Lumsdain, A. In Annual ACM Symposium on Parallelism in Algorithms and Architectures, pages 113-115, 2008.
Brief announcement: Leveraging non-blocking collective communication in high-performance applications [link]Website   doi   link   bibtex   abstract  
Optimizing non-blocking collective operations for InfiniBand. Hoefler, T.; and Lumsdaine, A. In IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM, 2008.
Optimizing non-blocking collective operations for InfiniBand [link]Website   doi   link   bibtex   abstract  
Accurately measuring collective operations at massive scale. Hoefler, T.; Schneider, T.; and Lumsdaine, A. In IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM, 2008.
Accurately measuring collective operations at massive scale [link]Website   doi   link   bibtex   abstract  
Overlapping communication and computation with high level communication routines. Hoefler, T.; and Lumsdaine, A. In Proceedings CCGRID 2008 - 8th IEEE International Symposium on Cluster Computing and the Grid, pages 572-577, 2008.
Overlapping communication and computation with high level communication routines [link]Website   doi   link   bibtex   abstract  
Sparse non-blocking collectives in quantum mechanical calculations. Hoefler, T.; Lorenzen, F.; and Lumsdaine, A. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5205 LNCS: 55-63. 2008.
Sparse non-blocking collectives in quantum mechanical calculations [link]Website   doi   link   bibtex   abstract  
Communication optimization for medical image reconstruction algorithms. Hoefler, T.; Schellmann, M.; Gorlatch, S.; and Lumsdaine, A. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5205 LNCS: 75-83. 2008.
Communication optimization for medical image reconstruction algorithms [link]Website   doi   link   bibtex   abstract  
Message progression in parallel computing - To thread or not to thread?. Hoefler, T.; and Lumsdaine, A. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, volume Proceeding, pages 213-222, 2008. Institute of Electrical and Electronics Engineers Inc.
Message progression in parallel computing - To thread or not to thread? [link]Website   doi   link   bibtex   abstract  
Adaptive routing strategies for modern high performance networks. Geoffray, P.; and Hoefler, T. In Proceedings - Symposium on the High Performance Interconnects, Hot Interconnects, pages 165-172, 2008.
Adaptive routing strategies for modern high performance networks [link]Website   doi   link   bibtex   abstract  
Demonstration of fast, single-packet radiolocation, applied to 802.11 wireless networking. Antolovic, D. In 2008 5th IEEE Consumer Communications and Networking Conference, CCNC 2008, pages 1219-1220, 2008.
Demonstration of fast, single-packet radiolocation, applied to 802.11 wireless networking [link]Website   doi   link   bibtex   abstract  
Architecture of a 802.11b access point with single-packet radiolocation. Antolovic, D. Technical Report 2008.
Architecture of a 802.11b access point with single-packet radiolocation [link]Website   link   bibtex   abstract  
Ranking web sites with real user traffic. Meiss, M., R.; Menczer, F.; Fortunato, S.; Flammini, A.; and Vespignani, A. In WSDM'08 - Proceedings of the 2008 International Conference on Web Search and Data Mining, pages 65-75, 2008.
Ranking web sites with real user traffic [link]Website   doi   link   bibtex   abstract  
Structural analysis of behavioral networks from the Internet. Meiss, M., R.; Menczer, F.; and Vespignani, A. Journal of Physics A: Mathematical and Theoretical, 41(22). 2008.
Structural analysis of behavioral networks from the Internet [link]Website   doi   link   bibtex   abstract  
Directional radio response of a 802.11b device guided by radiolocation. Antolovic, D. In PORTABLE-POLYTRONIC 2008 - 2nd IEEE International Interdisciplinary Conference on Portable Information Devices and the 2008 7th IEEE Conference on Polymers and Adhesives in Microelectronics and Photon, 2008.
Directional radio response of a 802.11b device guided by radiolocation [link]Website   doi   link   bibtex   abstract  
The LEAD-WxChallenge pilot project: enabling the community. Clark, R.; Marru, S.; Christie, M.; Gannon, D.; Illston, B.; Droegemeier, K.; and Baltzer, T. In 24th Conference on IIPS, 2008.
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Programming e-science gateways. Gannon, D. Making Grids Work,191-200. 2008.
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Monitoring and Managing E-Science Cyber-Infrastructures: A Case Study. Perera, S.; Marru, S.; and Gannon, D. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 402-403, 2008. IEEE
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A scalable and robust coordination architecture for distributed management. Perera, S.; and Gannon, D. Technical Report 2008.
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The Importance of Long-Term Science and Engineering Infrastructure for Digital Discovery. Wilkins-Diehr, N.; Alameda, J.; Droegemeier, K.; Gannon, D.; and Martin, S. submitted to the NSF’s Office of Cyberinfrastructure. 2008.
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Employing Automated Management to Administer a Large-Scale E-Science Cyber-Infrastructure. Perera, S.; Marru, S.; and Gannon, D. Retrieved oct, 21. 2008.
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Mapreduce for data intensive scientific analyses. Ekanayake, J.; Pallickara, S.; and Fox, G., C. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 277-284, 2008. IEEE
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A collaborative framework for scientific data analysis and visualization. Ekanayake, J.; Pallickara, S.; and Fox, G., C. In Collaborative Technologies and Systems, 2008. CTS 2008. International Symposium on, pages 339-346, 2008. IEEE
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An orchestration for distributed web service handlers. Yildiz, B.; Fox, G., C.; and Pallickara, S. In Internet and Web Applications and Services, 2008. ICIW'08. Third International Conference on, pages 638-643, 2008. IEEE
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Performance of Data Intensive Supercomputing Runtime Environments. Ekanayake, J.; Pallickara, S.; and Fox, G., C. Technical Report 2008.
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Collaborative Framework for Scientific Data Analysis. Ekanayake, J.; Pallickara, S.; and Fox, G., C. In Visualization,‖ The 2008 International Symposium on Collaborative Technologies and Systems, 2008.
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An overview of the granules runtime for cloud computing. Pallickara, S.; Ekanayake, J.; and Fox, G., C. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 412-413, 2008. IEEE
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A survey of distributed workflow characteristics and resource requirements. Ramakrishnan, L.; and Gannon, D. Indiana University,1-23. 2008.
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Lead cyberinfrastructure to track real-time storms using spruce urgent computing. Marru, S.; Gannon, D.; Nadella, S.; Beckman, P.; Weber, D., B.; Brewster, K., A.; and Droegemeier, K., K. CTWatch Quarterly, 4(1): 5-16. 2008.
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Building Virtual Organizations g g Around Supercomputing Grids and Clouds. Gannon, D. In The 6th International Conference on Computer Science & Education, 2008.
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Visual comparison of search results: A censorship case study. Meiss, M.; and Menczer, F. First Monday, 13(7). 2008.
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Query capabilities of the Karma provenance framework. Simmhan, Y., L.; Plale, B.; and Gannon, D. Concurrency and Computation: Practice and Experience, 20(5): 441-451. 2008.
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On the secure creation, organisation and discovery of topics in distributed publish/subscribe systems. Pallickara, S.; Fox, G., C.; and Gadgil, H. International journal of high performance computing and networking, 5(3): 156-167. 2008.
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ParaXML: a parallel XML processing model on the multicore CPUs, TR662. Wei, L.; Gannon, D.; Lu, W.; and Gannon, D. Technical Report 2008.
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Modeling and on-the-fly solutions for solid earth sciences: Web services and data portal for earthquake early warning system. Bock, Y.; Crowell, B.; Prawirodirdjo, L.; Jamason, P.; Chang, R.; Fang, P.; Squibb, M.; Pierce, M.; Gao, X.; Webb, F.; and others In Geoscience and Remote Sensing Symposium, 2008. IGARSS 2008. IEEE International, volume 4, pages IV--124, 2008.
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VLab: A Service Oriented Architecture for Distributed First Principles Materials Computations. da SIlva, C.; da Silveira, P.; Wentzcovitch, R.; Pierce, M.; and Erlebacher, G. In APS Meeting Abstracts, 2008.
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BioVLAB-microarray: Microarray data analysis in virtual environment. Yang, Y.; Choi, J., Y.; Choi, K.; Pierce, M.; Gannon, D.; and Kim, S. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 159-165, 2008.
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The problem solving environments of teraGrid, science gateways, and the intersection of the two. Basney, J.; Martin, S.; Navarro, J.; Pierce, M.; Scavo, T.; Strand, L.; Uram, T.; Wilkins-Diehr, N.; Wu, W.; and Youn, C. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 725-734, 2008.
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Open grid computing environment's workflow suite for e-science projects. Marru, S.; Pierce, M.; Herath, C.; and Perera, S. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 332-333, 2008.
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Change and Anomaly Detection in Real-Time GPS Data. Granat, R.; Pierce, M.; Gao, X.; and Bock, Y. In AGU Fall Meeting Abstracts, 2008.
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SQMD: Architecture for scalable, distributed database system built on virtual private servers. Kim, K.; Pierce, M., E.; and Guha, R. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 658-665, 2008.
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New science on the Open Science Grid. Pordes, R.; Altunay, M.; Avery, P.; Bejan, A.; Blackburn, K.; Blatecky, A.; Gardner, R.; Kramer, B.; Livny, M.; McGee, J.; Potekhin, M.; Quick, R.; Olson, D.; Roy, A.; Sehgal, C.; Wenaus, T.; Wilde, M.; and Würthwein, F. Journal of Physics: Conference Series, 125. 2008.
New science on the Open Science Grid [link]Website   doi   link   bibtex   abstract  
The open science grid status and architecture. Pordes, R.; Petravick, D.; Kramer, B.; Olson, D.; Livny, M.; Roy, A.; Avery, P.; Blackburn, K.; Wenaus, T.; Würthwein, F.; Foster, I.; Gardner, R.; Wilde, M.; Blatecky, A.; McGee, J.; and Quick, R. Journal of Physics: Conference Series, 119(5). 2008.
The open science grid status and architecture [link]Website   doi   link   bibtex   abstract  
Riding the geoscience cyberinfrastructure wave of data: Real time data use in education workshop. Plale, B.; and Cao, B. In 4th IEEE International Conference on eScience, eScience 2008, pages 456, 2008.
Riding the geoscience cyberinfrastructure wave of data: Real time data use in education workshop [link]Website   doi   link   bibtex   abstract  
An implementation of a query language with generalized quantifiers. Badia, A.; Debes, B.; and Cao, B. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5231 LNCS: 547-548. 2008.
An implementation of a query language with generalized quantifiers [link]Website   doi   link   bibtex   abstract  
Provenance collection in an industry biochemical discovery cyberinfrastructure. Cao, B.; Subramanian, G.; Doddapaneni, S.; and Plale, B. In Fourth IEEE International Conference on eScience, eScience 2008, pages 424-425, 2008.
Provenance collection in an industry biochemical discovery cyberinfrastructure [link]Website   doi   link   bibtex   abstract  
Architecture for scalable, distributed database system built on multicore servers. Kim, K.; Guha, R.; Pierce, M.; Fox, G., C.; Wild, D.; and Gilbert, K. Technical Report Tech. rep. Indiana University, Bloomington, USA, 2008.
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Principles and experiences: building a hybrid metadata service for Service Oriented Architecture based grid applications. Aktas, M., S.; Fox, G., C.; and Pierce, M. In Third International IEEE International Conference on Internet and Web Applications and Services ICIW, volume 8, pages 8-13, 2008.
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Distributed high performance grid information service. Aktas, M., S.; Fox, G., C.; and Pierce, M., E. Submitted ot Journal of Systems and Software. 2008.
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Whither Spatial Cyberinfrastructure?. Pierce, M., E.; Fox, G., C.; Ma, Y.; Wang, J.; Kedar, S.; Moe, K.; Gannon, D.; Jim Myers, N.; and Shantenu Jha, L., S., U. Technical Report 2008.
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Information federation in grids. Aktas, M., S.; Fox, G., C.; and Pierce, M. In Semantics, Knowledge and Grid, 2008. SKG'08. Fourth International Conference on, pages 109-116, 2008.
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SWARM: Scheduling Large-Scale Jobs over the Loosely-Coupled HPC Clusters. Pallickara, S., L.; and Pierce, M. In eScience, 2008. eScience'08. IEEE Fourth International Conference on, pages 285-292, 2008.
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Editorial Introduction: Special Issue on Grids and Geospatial Information Systems. Pierce, M., E. Concurrency and Computation: Practice and Experience, 20(14). 2008.
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Special Issue Editorial Introduction: Grids and Geospatial Information Systems. Pierce, M., E. Concurrency and Computation: Practice and Experience, 20(14): 1611-1615. 2008.
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Cyberaide JavaScript: A JavaScript commodity. von Laszewski, G.; Wang, F.; Younge, A.; He, X.; Guo, Z.; and Pierce, M. In Grid Computing Environments Workshop, 2008. GCE'08, pages 1-10, 2008.
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VLab: Collaborative Grid Services and Portals to Support Computational Mineral Physics. da Silveira, P., R.; da Silva, C., R.; Karki, B., B.; Wentzcovitch, R.; Pierce, M., E.; and Erlebacher, G. In AGU Fall Meeting Abstracts, 2008.
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Collective collaborative tagging system. Choi, J., Y.; Rosen, J.; Maini, S.; Pierce, M., E.; and Fox, G., C. In Grid Computing Environments Workshop, 2008. GCE'08, pages 1-7, 2008.
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Quakesim: Web services, portals, and infrastructure for geophysics. Pierce, M., E.; Fox, G., C.; Aydin, G.; Qi, Z.; Donnellan, A.; Parker, J., W.; and Granat, R. In Aerospace Conference, 2008 IEEE, pages 1-7, 2008.
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Social networking for scientists using tagging and shared bookmarks: a Web 2.0 application. Pierce, M., E.; Fox, G., C.; Rosen, J.; Maini, S.; and Choi, J., Y. In Collaborative Technologies and Systems, 2008. CTS 2008. International Symposium on, pages 257-266, 2008.
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CINF 64-High performance robust datamining for cheminformatics. Fox, G., C.; Bae, S.; Guha, R.; Pierce, M.; Qiu, X.; Wild, D., J.; and Yuan, H. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 235, 2008.
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QuakeSim: Efficient Modeling of Sensor Web Data in a Web Services Environment. Donnellan, A.; Parker, J.; Granat, R.; Fox, G., C.; Pierce, M.; Rundle, J.; McLeod, D.; Al-Ghanmi, R.; Grant, L.; and Brooks, W. In Aerospace Conference, 2008 IEEE, pages 1-11, 2008.
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CINF 23-I don't care where my data and methods are: A web-service approach for distributed access to methods, data and models. Guha, R.; Fox, G., C.; Gilbert, K., E.; Pierce, M.; and Wild, D., J. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 235, 2008.
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Cyberinfrastructure resources for U.S. Scholarship. Simms, S., C.; Stewart, C., A.; and McCaulay, S., D. In Proceedings of the 36th annual ACM SIGUCCS conference on User services conference - SIGUCCS '08, pages 341, 2008. ACM Press
Cyberinfrastructure resources for U.S. Scholarship [link]Website   doi   link   bibtex   abstract  
The QuakeSim project: Web services for managing geophysical data and applications. Pierce, M., E.; Fox, G., C.; Aktas, M., S.; Aydin, G.; Gadgil, H.; Qi, Z.; and Sayar, A. Earthquakes: Simulations, Sources and Tsunamis, pages 635-651. Birkhäuser Basel, 2008.
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TeraGrid: Analysis of organization, system architecture, and middleware enabling new types of applications. Catlett, C.; Allcock, W., E.; Andrews, P.; Aydt, R.; Bair, R.; Balac, N.; Banister, B.; Barker, T.; Bartelt, M.; Beckman, P.; Berman, F.; Bertoline, G.; Blatecky, A.; Boisseau, J.; Bottum, J.; Brunett, S.; Bunn, J.; Butler, M.; Carver, D.; Cobb, J.; Cockerill, T.; Couvares, P.; Dahan, M.; Diehl, D.; Dunning, T.; Foster, I.; Gaither, K.; Gannon, D.; Goasguen, S.; Grobe, M.; Hart, D.; Heinzel, M.; Hempel, C.; Huntoon, W.; Insley, J.; Jordan, C.; Judson, I.; Kamrath, A.; Karonis, N.; Kesselman, C.; Kovatch, P.; Lane, L.; Lathrop, S.; Levine, M.; Lifka, D.; Liming, L.; Livny, M.; Loft, R.; Marcusiu, D.; Marsteller, J.; Martin, S.; McCaulay, S.; McGee, J.; McGinnis, L.; McRobbie, M.; Messina, P.; Moore, R.; Moore, R.; Navarro, J.; Nichols, J.; Papka, M.; Pennington, R.; Pike, G.; Pool, J.; Reddy, R.; Reed, D.; Rimovsky, T.; Roberts, E.; Roskies, R.; Sanielevici, S.; Scott, J.; Shankar, A.; Sheddon, M.; Showerman, M.; Simmel, D.; Singer, A.; Skow, D.; Smallen, S.; Smith, W.; Song, C.; Stevens, R.; Stewart, C.; Stock, R.; Stone, N.; Towns, J.; Urban, T.; Vildibill, M.; Walker, E.; Welch, V.; Wilkins-Diehr, N.; Williams, R.; Winkler, L.; Zhao, L.; and Zimmerman, A. Volume 16 2008.
TeraGrid: Analysis of organization, system architecture, and middleware enabling new types of applications [link]Website   link   bibtex   abstract  
Building and applying geographical information system Grids. Aktas, M., S.; Aydin, G.; Bulut, H.; Fox, G., C.; Gadgil, H.; Ko, S.; Pierce, M., E.; Sayar, A.; Gadgil, H.; Aktas, M., S.; Fox, G., C.; Ko, S.; Bulut, H.; Pierce, M., E.; Aydin, G.; Bulut, H.; Fox, G., C.; Gadgil, H.; Ko, S.; Pierce, M., E.; and Sayar, A. Concurrency and Computation: Practice and Experience, 20(14): 1653-1695. 2008.
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  2007 (67)
NLOPredict: visualization and data analysis software for nonlinear optics. Moad, A., J.; Moad, C., W.; Perry, J., M.; Wampler, R., D.; Goeken, G., S.; Begue, N., J.; Shen, T.; Heiland, R.; and Simpson, G., J. Journal of computational chemistry, 28(12): 1996-2002. 2007.
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Visual methods for interpreting optical nonlinearity at the molecular level. Wampler, R., D.; Moad, A., J.; Moad, C., W.; Heiland, R.; and Simpson, G., J. Accounts of chemical research, 40(10): 953-960. 2007.
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MutDB: update on development of tools for the biochemical analysis of genetic variation. Singh, A.; Olowoyeye, A.; Baenziger, P., H.; Dantzer, J.; Kann, M., G.; Radivojac, P.; Heiland, R.; and Mooney, S., D. Nucleic acids research, 36(suppl_1): D815-D819. 2007.
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VisPort: Web-Based Access to Community-Specific Visualization Functionality. Baker, M., P.; Heiland, R.; Bachta, E.; and Das, M. In TeraGrid, 2007.
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A practically constant-time MPI broadcast algorithm for large-scale InfiniBand clusters with multicast. Hoefler, T.; Siebert, C.; and Rehm, W. In Proceedings - 21st International Parallel and Distributed Processing Symposium, IPDPS 2007; Abstracts and CD-ROM, 2007.
A practically constant-time MPI broadcast algorithm for large-scale InfiniBand clusters with multicast [link]Website   doi   link   bibtex   abstract  
Optimizing a conjugate gradient solver with non-blocking collective operations. Hoefler, T.; Gottschling, P.; Lumsdaine, A.; and Rehm, W. Parallel Computing, 33(9): 624-633. 2007.
Optimizing a conjugate gradient solver with non-blocking collective operations [link]Website   doi   link   bibtex   abstract  
Implementation and performance analysis of non-blocking collective operations for MPI. Hoefler, T.; Lumsdaine, A.; and Rehm, W. In Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, SC'07, 2007.
Implementation and performance analysis of non-blocking collective operations for MPI [link]Website   doi   link   bibtex   abstract  
Netgauge: A network performance measurement framework. Hoefler, T.; Mehlan, T.; Lumsdaine, A.; and Rehm, W. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4782 LNCS: 659-671. 2007.
Netgauge: A network performance measurement framework [link]Website   link   bibtex   abstract  
A new approach to MPI collective communication implementations. Hoefler, T.; Squyres, J., M.; Fagg, G., E.; Bosilca, G.; Rehm, W.; and Lumsdaine, A. Springer US, 2007.
A new approach to MPI collective communication implementations [link]Website   doi   link   bibtex   abstract  
Low-overhead LogGP parameter assessment for modern interconnection networks. Hoefler, T.; Lichei, A.; and Rehm, W. In Proceedings - 21st International Parallel and Distributed Processing Symposium, IPDPS 2007; Abstracts and CD-ROM, 2007.
Low-overhead LogGP parameter assessment for modern interconnection networks [link]Website   doi   link   bibtex   abstract  
A case for standard non-blocking collective operations. Hoefler, T.; Kambadur, P.; Graham, R., L.; Shipman, G.; and Lumsdaine, A. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4757 LNCS: 125-134. 2007.
A case for standard non-blocking collective operations [link]Website   link   bibtex   abstract  
Design of a Radio-Frequency Multiplexer, Used in Radiolocation of 802.11 Wireless Sources. Antolovic, D.; and Wallace, S., S. In 2007 IEEE International Conference on Portable Information Devices, PIDs 2007, 2007. Institute of Electrical and Electronics Engineers Inc.
Design of a Radio-Frequency Multiplexer, Used in Radiolocation of 802.11 Wireless Sources [link]Website   doi   link   bibtex   abstract  
Intercellular Genomics of Subsurface Microbial Colonies. Ortoleva, P.; Tuncay, K.; Gannon, D.; and Meile, C. Technical Report 2007.
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The Center for Component Technology for Terascale Software Simulation (CCTTSS) at Indiana University. Gannon, D.; and Bramley, R. Technical Report 2007.
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V-lab-protein: Virtual collaborative lab for protein sequence analysis. Choi, J., Y.; Yang, Y.; Kim, S.; and Gannon, D. In Bioinformatics and Biomedicine Workshops, 2007. BIBMW 2007. IEEE International Conference on, pages 183-190, 2007. IEEE
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The LEAD science portal problem solving environment. Gannon, D.; Plale, B.; Christie, M.; Marru, S.; Kandaswamy, G.; Fang, L.; Huang, Y.; Lee-Palickara, S.; Jenson, S.; and Liu, N. In Proceedings of AMS Conference, 2007.
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Programming Paradigms for Scientific Problem Solving Environments. Gannon, D.; Christie, M.; Marru, S.; Shirasuna, S.; and Slominski, A. Grid-Based Problem Solving Environments, pages 3-15. Springer, 2007.
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LEAD at the Unidata workshop: demonstrating democratization of NWP capabilities. Baltzer, T.; Wilson, A.; Ramamurthy, M.; Marru, S.; Christie, M.; Gannon, D.; Rossi, A.; Hampton, S.; Alameda, J.; and Droegemeier, K. In 23rd Conference on IIPS, 2007.
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A hybrid decomposition scheme for building scientific workflows. Lu, W.; Chiu, K.; Shirasuna, S.; and Gannon, D. In Proceedings of the 2007 spring simulation multiconference-Volume 2, pages 388-394, 2007. Society for Computer Simulation International
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Fault-tolerant reliable delivery of messages in distributed publish/subscribe systems. Pallickara, S.; Bulut, H.; and Fox, G., C. In Autonomic Computing, 2007. ICAC'07. Fourth International Conference on, pages 19, 2007. IEEE
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A scalable approach for the secure and authorized tracking of the availability of entities in distributed systems. Pallickara, S.; Ekanayake, J.; and Fox, G., C. In Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International, pages 1-10, 2007. IEEE
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Building grid portals for e-science: A service oriented architecture. Gannon, D.; Plale, B.; Christie, M.; Huang, Y.; Jensen, S.; Liu, N.; Marru, S.; Pallickara, S., L.; Perera, S.; and Shirasuna, S. High Performance Computing and Grids in Action. 2007.
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Data management in dynamic environment-driven computational science. Simmhan, Y., L.; Pallickara, S., L.; Vijayakumar, N., N.; and Plale, B. Grid-based problem solving environments, pages 317-333. Springer, 2007.
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ROOTlets and Pythia: Grid enabling HEP applications using the Clarens Toolkit. Steenberg, C.; Ekanayake, J.; Fox, G., C.; Kahn, F.; Lederman, A.; Litvin, V.; Legrand, I.; Newman, H.; Pallickara, S.; and Thomas, M. In Proceedings of Computing for High Energy Physics, pages 2-9, 2007.
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Parallel XML processing by work stealing. Lu, W.; and Gannon, D. In Proceedings of the 2007 workshop on Service-oriented computing performance: aspects, issues, and approaches, pages 31-38, 2007. ACM
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Workflows for eScience. Gannon, D.; Deelman, E.; Taylor, I.; and Shields, M. Introduction. Springer: Berlin,1-9. 2007.
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Examining the challenges of scientific workflows. Gil, Y.; Deelman, E.; Ellisman, M.; Fahringer, T.; Fox, G., C.; Gannon, D.; Goble, C.; Livny, M.; Moreau, L.; and Myers, J. Computer, 40(12). 2007.
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The impact of multicore on computational science software. Dongarra, J.; Gannon, D.; Fox, G., C.; and Kennedy, K. CTWatch Quarterly, 3(1): 1-10. 2007.
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VisPort: Web-Based Access to Community-Specific Visualization Functionality [Shedding New Light on Exploding Stars: Visualization for TeraScale Simulation of Neutrino-Driven Supernovae (Final Technical Report)]. Baker, M., P. Technical Report 2007.
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A framework for analysis of anonymized network flow data. Meiss, M.; Menczer, F.; and Vespignani, A. In Proceedings of the NSF Symposium on Next Generation of Data Mining and Cyber-Enabled Discovery for Innovation, 2007.
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Progress Towards Petascale Applications in Biology: Status in 2006. Stewart, C., A.; Müller, M.; and Lingwall, M. In Euro-Par 2006: Parallel Processing, volume 4375 LNCS, pages 289-303, 2007. Springer Berlin Heidelberg
Progress Towards Petascale Applications in Biology: Status in 2006 [link]Website   doi   link   bibtex   abstract  
Virtual laboratory for planetary materials: System service architecture overview. Da Silva, C., R., S.; da Silveira, P., R., C.; Karki, B.; Wentzcovitch, R., M.; Jensen, P., A.; Bollig, E., F.; Pierce, M.; Erlebacher, G.; and Yuen, D., A. Physics of the Earth and Planetary Interiors, 163(1): 321-332. 2007.
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VLab: a service oriented architecture for first principles computations of planetary materials properties. da Silva, C., R.; da Silveira, P.; Wentzcovitch, R., M.; Pierce, M.; and Erlebacher, G. In AGU Fall Meeting Abstracts, 2007.
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JavaScript Grid Abstractions. Laszewski, G.; Wang, F.; Younge, A.; Guo, Z.; Von Laszewski, G.; Wang, F.; Younge, A.; Guo, Z.; Pierce, M.; Laszewski, G.; Wang, F.; Younge, A.; Guo, Z.; Von Laszewski, G.; Wang, F.; Younge, A.; Guo, Z.; and Pierce, M. In Proceedings of the Gr id Comput ing Environme nts (GCE) workshop, pages 11-12, 2007.
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Special section: Semantic grid and knowledge grid Guest Editor: Hai Zhuge. Zhuge, H.; Shen, J.; Grossmann, G.; Yang, Y.; Stumptner, M.; Schrefl, M.; Reiter, T.; Dimkovski, M.; Deeb, K.; Kim, K., H.; and others Future Generation Computer Systems, 23(3): 281-283. 2007.
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Detection of regional events using streaming GPS. Granat, R.; Pierce, M.; Gao, X.; and Bock, Y. In AGU Fall Meeting Abstracts, 2007.
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A multinational deployment of 3D laser scanning to study craniofacial dysmorphology in fetal alcohol spectrum disorders. Rogers, J.; Wernert, E.; Moore, E.; Ward, R.; Wetherill, L., F.; and Foroud, T. In Proceedings of SPIE - The International Society for Optical Engineering, volume 6491, 2007.
A multinational deployment of 3D laser scanning to study craniofacial dysmorphology in fetal alcohol spectrum disorders [link]Website   link   bibtex   abstract  
I/O induced scalability limits of bioinformatics applications. Henschel, R.; and Müller, M., S. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, pages 609-613, 2007.
I/O induced scalability limits of bioinformatics applications [link]Website   doi   link   bibtex   abstract  
Empowering distributed workflow with the data capacitor: maximizing lustre performance across the wide area network. Simms, S., C.; Pike, G., G.; Teige, S.; Hammond, B.; Ma, Y.; Simms, L., L.; Westneat, C.; and Balog, D., A. In Proceedings of the 2007 workshop on Service-oriented computing performance: aspects, issues, and approaches, pages 53-58, 2007. ACM
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The open science grid. Pordes, R.; Petravick, D.; Kramer, B.; Olson, D.; Livny, M.; Roy, A.; Avery, P.; Blackburn, K.; Wenaus, T.; Würthwein, F.; Foster, I.; Gardner, R.; Wilde, M.; Blatecky, A.; McGee, J.; and Quick, R. Journal of Physics: Conference Series, 78(1). 2007.
The open science grid [link]Website   doi   link   bibtex   abstract  
Implementation of a distributed architecture for managing collection and dissemination of data for fetal alcohol spectrum disorders research. Arenson, A.; Bakhireva, L.; Chambers, T.; Deximo, C.; Foroud, T.; Jacobson, J.; Jacobson, S.; Jones, K.; Mattson, S.; May, P.; Moore, E.; Ogle, K.; Riley, E.; Robinson, L.; Rogers, J.; Streissguth, A.; Tavares, M.; Urbanski, J.; Yezerets, H.; and Stewart, C. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), volume 4360 LNBI, pages 33-44, 2007.
Implementation of a distributed architecture for managing collection and dissemination of data for fetal alcohol spectrum disorders research [link]Website   link   bibtex   abstract  
Wide area filesystem performance using lustre on the teragrid. Simms, S., C.; Pike, G., G.; and Balog, D. Technical Report 2007.
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Scalable, fault-tolerant management of grid services. Gadgil, H.; Fox, G., C.; Pallickara, S.; and Pierce, M. In Cluster Computing, 2007 IEEE International Conference on, pages 349-356, 2007.
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Implementing a caching and tiling map server: a web 2.0 case study. Liu, Z.; Pierce, M., E.; Fox, G., C.; and Devadasan, N. In Collaborative Technologies and Systems, 2007. CTS 2007. International Symposium on, pages 247-256, 2007.
link   bibtex  
GTLAB: grid tag libraries supporting workflows within science gateways. Nacar, M., A.; Pierce, M., E.; and Fox, G., C. In Semantics, Knowledge and Grid, Third International Conference on, pages 194-199, 2007.
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Matchmaking scientific workflows in grid environments. Gong, Y.; Pierce, M., E.; and Fox, G., C. In 20th IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS 2007), Cambridge, MA (November 2007), 2007.
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Scalable, fault-tolerant management in a service oriented architecture. Gadgil, H.; Fox, G., C.; Pallickara, S.; and Pierce, M. In Proceedings of the 16th international symposium on High performance distributed computing, pages 235-236, 2007.
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Grids meet too much computing, too much data and never too much simplicity. Fox, G., C.; and Pierce, M. White Paper. 2007.
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Extending GTLAB Tag Libraries for Grid Workflows. Nacar, M., A.; Pierce, M., E.; and Fox, G., C. Semantics, Knowledge and Grid, Third International Conference on. 2007.
doi   link   bibtex  
Web service infrastructure for chemoinformatics. Xiao, D.; Gilbert, K., E.; Guha, R.; Heiland, R.; Jungkee, K.; Pierce, M., E.; Fox, G., C.; Wild, D., J.; Dong, X.; Gilbert, K., E.; Guha, R.; Heiland, R.; Kim, J.; Pierce, M., E.; Fox, G., C.; and Wild, D., J. Journal of chemical information and modeling, 47(4): 1303-1307. 2007.
Web service infrastructure for chemoinformatics [link]Website   doi   link   bibtex   abstract  
Final Report for DOE Project: Portal Web Services: Support of DOE SciDAC Collaboratories. Mary Thomas, P., I.; Geoffrey Fox, C.; Gannon, D.; Pierce, M.; Moore, R.; Schissel, D.; and Boisseau, J. Technical Report The University of Texas, Texas Advanced Computing Center; Austin, TX; General Atomics, San Diego, CA; Indiana University, Bloomington, IN; San Diego State University, San Diego, CA, 2007.
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VLAB: Web services, portlets, and workflows for enabling cyber-infrastructure in computational mineral physics. Bollig, E., F.; Jensen, P., A.; Lyness, M., D.; Nacar, M., A.; da Silveira, P., R., C.; Kigelman, D.; Erlebacher, G.; Pierce, M.; Yuen, D., A.; and da Silva, C., R., S. Physics of the Earth and Planetary Interiors, 163(1): 333-346. 2007.
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The Open Grid Computing Environments collaboration: portlets and services for science gateways. Alameda, J.; Christie, M.; Fox, G., C.; Futrelle, J.; Gannon, D.; Hategan, M.; Kandaswamy, G.; von Laszewski, G.; Nacar, M., A.; Pierce, M.; and others Concurrency and Computation: Practice and Experience, 19(6): 921-942. 2007.
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Ontology-based Information Management in QuakeSim. Al-Ghanmi, R.; McLeod, D.; Grant, L.; Donnellan, A.; Parker, J.; and Pierce, M. In AGU Fall Meeting Abstracts, 2007.
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Analysis of streaming GPS measurements of surface displacement through a web services environment. Granat, R.; Aydin, G.; Pierce, M.; Qi, Z.; and Bock, Y. In Computational Intelligence and Data Mining, 2007. CIDM 2007. IEEE Symposium on, pages 750-757, 2007.
link   bibtex  
Building QuakeSim portlets with GTLAB. Nacar, M., A.; Pierce, M., E.; Donnellan, A.; and Fox, G., C. In International Workshop on Grid Computing Environments, 2007.
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Building a sensor grid for real time global positioning system data. Aydin, G.; Qi, Z.; Pierce, M., E.; Bock, Y.; and Fox, G., C. In Proc. Workshop on Principles of Pervasive Information Systems Design Sunday, 2007.
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Building a grid portal for TeraGrid's Big Red. Nacar, M., A.; Choi, J., Y.; Pierce, M., E.; and Fox, G., C. Proceedings of TeraGrid, 2007. 2007.
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Web 2.0 for e-science environments. Fox, G., C.; Pierce, M., E.; Mustacoglu, A., F.; and Topcu, A., E. In Semantics, Knowledge and Grid, Third International Conference on, pages 1-6, 2007.
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QuakeSim: Enabling Model Interactions in Solid Earth Science Sensor Webs. Donnellan, A.; Parker, J.; Norton, C.; Lyzenga, G.; Glasscoe, M.; Fox, G., C.; Pierce, M.; Rundle, J.; McLeod, D.; Grant, L.; and others In Aerospace Conference, 2007 IEEE, pages 1-8, 2007.
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QuakeSim: Enabli model interactions in solid earth science sensor webs. Donnellan, A.; Parker, J.; Norton, C.; Lyzenga, G.; Glasscoe, M.; Fox, G., C.; Pierce, M.; Rundle, J.; McLeod, D.; Grant, L.; Brooks, W.; and Tullis, T. In IEEE Aerospace Conference Proceedings, 2007.
QuakeSim: Enabli model interactions in solid earth science sensor webs [link]Website   doi   link   bibtex   abstract  
Architecture, performance, and scalability of a real-time global positioning system data grid. Aydin, G.; Qi, Z.; Pierce, M., E.; Fox, G., C.; and Bock, Y. Physics of the Earth and Planetary Interiors, 163(1): 347-359. 2007.
link   bibtex  
High throughput image analysis on PetaFLOPS systems. Henschel, R.; Müller, M.; and Kalaidzidis, Y. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 4375 LNCS: 323-329. 2007.
High throughput image analysis on PetaFLOPS systems [link]Website   link   bibtex   abstract  
Fault tolerant high performance Information Services for dynamic collections of Grid and Web services. Aktas, M., S.; Fox, G., C.; and Pierce, M. Future Generation Computer Systems, 23(3): 317-337. 2007.
Fault tolerant high performance Information Services for dynamic collections of Grid and Web services [link]Website   doi   link   bibtex  
VLab: collaborative grid services and portals to support computational material science. Nacar, M., A.; Aktas, M., S.; Pierce, M.; Lu, Z.; Erlebacher, G.; Kigelman, D.; Bollig, E., F.; da Silva, C., R., S.; Sowell, B.; and Yuen, D., A. Concurrency and Computation: Practice and Experience, 19(12): 1717-1728. 2007.
VLab: collaborative grid services and portals to support computational material science [pdf]Website   doi   link   bibtex  
Report of the Indiana University Research Data Management Taskforce. Technical Report 2007.
Report of the Indiana University Research Data Management Taskforce [pdf]Paper   Report of the Indiana University Research Data Management Taskforce [link]Website   link   bibtex   abstract  
  2006 (74)
XML for BioinformaticsEthan CeramiBerlin: Springer-Verlag; ISBN: 0-387-23028-9; 304pp.; 2005;£ 42.50. Heiland, R. Briefings in Bioinformatics,125. 2006.
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Identification of similar regions of protein structures using integrated sequence and structure analysis tools. Peters, B.; Moad, C.; Youn, E.; Buffington, K.; Heiland, R.; and Mooney, S. BMC structural biology, 6(1): 4. 2006.
link   bibtex  
Instrument monitoring, data sharing, and archiving using Common Instrument Middleware Architecture (CIMA). Bramley, R.; Chiu, K.; Devadithya, T.; Gupta, N.; Hart, C.; Huffman, J., C.; Huffman, K.; Ma, Y.; and McMullen, D., F. Journal of Chemical Information and Modeling, 46(3): 1017-1025. 2006.
Instrument monitoring, data sharing, and archiving using Common Instrument Middleware Architecture (CIMA) [link]Website   doi   link   bibtex   abstract  
A dynamic filtering technique for Sebek system monitoring. Balas, E.; Travis, G.; and Viecco, C. In Proceedings of the 2006 IEEE Workshop on Information Assurance, volume 2006, pages 275-282, 2006.
A dynamic filtering technique for Sebek system monitoring [link]Website   link   bibtex   abstract  
Single-packet radiolocation of 802.11 wireless sources, using an array of stationary antennas and high-speed RF multiplexing. Antolovic, D.; and Wallace, S., S. In ACM International Conference Proceeding Series, volume 220, 2006.
Single-packet radiolocation of 802.11 wireless sources, using an array of stationary antennas and high-speed RF multiplexing [link]Website   doi   link   bibtex   abstract  
An Introduction to Grids and Science Portals. Gannon, D.; and Plale, B. 2006.
link   bibtex  
Opportunities and challenges for future generation grid research. Gannon, D. In International Conference on High-Performance Computing, pages 2-3, 2006. Springer
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Unidata Workshop: Demonstrating Democratization of Numerical Weather Prediction Capabilities Using Linked Environments for Atmospheric Discovery (LEAD) Capabilities. Baltzer, T.; Wilson, A.; Marru, S.; Rossi, A.; Christi, M.; Hampton, S.; Gannon, D.; Alameda, J.; Ramamurthy, M.; and Droegemeier, K. In AGU Fall Meeting Abstracts, 2006.
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Extensible Terascale Facility (ETF): Indiana-Purdue Grid (IP-Grid). McRobbie, M.; Fox, G., C.; Gannon, D.; Palakal, M., J.; and Stewart, C. Technical Report 2006.
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A flexible and efficient approach to reconcile different web services-based event notification specifications. Huang, Y.; and Gannon, D. In Web Services, 2006. ICWS'06. International Conference on, pages 735-742, 2006. IEEE
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Bioacoustics of fishes of the family Sciaenidae (croakers and drums). Ramcharitar, J.; Gannon, D., P.; and Popper, A., N. Transactions of the American Fisheries Society, 135(5): 1409-1431. 2006.
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Report on the 2006 NSF Workshop on Challenges of Scientific Workflows. Gil, Y.; Deelman, E.; Ellisman, M.; Fahringer, T.; Fox, G., C.; Gannon, D.; Goble, C.; Livny, M.; Moreau, L.; and Myers, J. Technical Report 2006.
link   bibtex  
A hybrid XML-relational grid metadata catalog. Jensen, S.; Plale, B.; Pallickara, S., L.; and Sun, Y. In Parallel Processing Workshops, 2006. ICPP 2006 Workshops. 2006 International Conference on, pages 8-pp, 2006. IEEE
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Ws-messenger: A web services-based messaging system for service-oriented grid computing. Huang, Y.; Slominski, A.; Herath, C.; and Gannon, D. In Cluster Computing and the Grid, 2006. CCGRID 06. Sixth IEEE International Symposium on, volume 1, pages 8-pp, 2006. IEEE
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A framework for collecting provenance in data-centric scientific workflows. Simmhan, Y., L.; Plale, B.; and Gannon, D. In Web Services, 2006. ICWS'06. International Conference on, pages 427-436, 2006. IEEE
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A comparative study of web services-based event notification specifications. Huang, Y.; and Gannon, D. In Parallel Processing Workshops, 2006. ICPP 2006 Workshops. 2006 International Conference on, pages 8-pp, 2006. IEEE
link   bibtex  
Towards a quality model for effective data selection in collaboratories. Simmhan, Y., L.; Plale, B.; and Gannon, D. In Data Engineering Workshops, 2006. Proceedings. 22nd International Conference on, pages 72, 2006. IEEE
link   bibtex  
Building a generic SOAP framework over binary XML. Lu, W.; Chiu, K.; and Gannon, D. In High Performance Distributed Computing, 2006 15th IEEE International Symposium on, pages 195-204, 2006. IEEE
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A mechanism for creating scientific application services on-demand from workflows. Kandaswamy, G.; and Gannon, D. In Parallel Processing Workshops, 2006. ICPP 2006 Workshops. 2006 International Conference on, pages 8-pp, 2006. IEEE
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Enabling Web Service extensions for scientific workflows. Perera, S.; and Gannon, D. In Workflows in Support of Large-Scale Science, 2006. WORKS'06. Workshop on, pages 1-10, 2006. IEEE
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Mapping the diffusion of scholarly knowledge among major US research institutions. Börner, K.; Penumarthy, S.; Meiss, M.; and Ke, W. Scientometrics, 68(3): 415-426. 2006.
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Special issue: Workflow in grid systems. Fox, G., C.; and Gannon, D. Concurrency and Computation: Practice and Experience, 18(10): 1009-1019. 2006.
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Building web services for scientific grid applications. Kandaswamy, G.; Fang, L.; Huang, Y.; Shirasuna, S.; Marru, S.; and Gannon, D. IBM Journal of Research and Development, 50(2.3): 249-260. 2006.
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Casa and lead: Adaptive cyberinfrastructure for real-time multiscale weather forecasting. Plale, B.; Gannon, D.; Brotzge, J.; Droegemeier, K.; Kurose, J.; McLaughlin, D.; Wilhelmson, R.; Graves, S.; Ramamurthy, M.; and Clark, R., D. Computer, 39(11). 2006.
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Performance evaluation of the karma provenance framework for scientific workflows. Simmhan, Y.; Plale, B.; Gannon, D.; and Marru, S. Provenance and Annotation of Data,222-236. 2006.
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End-to-end trustworthy data access in data-oriented scientific computing. Pallickara, S., L.; Plale, B.; Fang, L.; and Gannon, D. In Cluster Computing and the Grid, 2006. CCGRID 06. Sixth IEEE International Symposium on, volume 1, pages 4-pp, 2006. IEEE
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Enabling End-to-End Trustworthiness in Data-Oriented Scientific Computing. Pallickara, S., L.; and Plale, B. In Proceedings of the Workshop on Web Services-based Grid Applications (WGSA’06) in association with the International Conference on Parallel Processing (ICPP-06), 2006.
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TrustCell: towards the end-to-end trustworthiness in data-oriented scientific computing. Pallickara, S., L.; and Plale, B. In Parallel Processing Workshops, 2006. ICPP 2006 Workshops. 2006 International Conference on, pages 8-pp, 2006. IEEE
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Experiences in Deploying Services within the Axis Container. Yildiz, B.; Pallickara, S.; and Fox, G., C. In Telecommunications, 2006. AICT-ICIW'06. International Conference on Internet and Web Applications and Services/Advanced International Conference on, pages 168, 2006. IEEE
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Trust Cell: Towards the End-to-End Trust in Data-Oriented Scientific Computing. Pallickara, S., L.; Plale, B.; Fang, L.; and Gannon, D. IEEE Cluster Computing and Grid (CCGrid). 2006.
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Dynamic, adaptive workflows for mesoscale meteorology. Gannon, D.; Plale, P.; Marru, S.; Kandaswamy, G.; Simmhan, Y., L.; Shirasuna, S.; Plale, B.; Marru, S.; Kandaswamy, G.; Simmhan, Y., L.; Shirasuna, S.; Plale, P.; Marru, S.; Kandaswamy, G.; Simmhan, Y., L.; and Shirasuna, S. Workflows for e-Science,126-142. 2006.
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Personal Workspace for Large-Scale Data-Driven Computational Experiment. Sun, Y.; Jensen, S.; Pallickara, S., L.; Plale, B.; Sun, Y.; Jensen, S.; Pallickara, S., L.; and Plale, B. In Proceedings of the 7th IEEE/ACM International Conference on Grid Computing, pages 112-119, 2006. IEEE
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A survey of the role and use of web services and service oriented architectures in scientific. Fox, G., C.; and Gannon, D. Technical Report 2006.
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Earth Science Community IT Resources through a Unified Data and Analysis Portal. Bock, Y.; Webb, F., H.; Kedar, S.; Pierce, M.; Scharber, M.; Argus, D., F.; Aydin, G.; Chang, R.; Dong, D.; Fang, P.; and others In AGU Fall Meeting Abstracts, 2006.
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GPS Sensor Web Time Series Analysis Using SensorGrid Technology. Granat, R.; Pierce, M.; Aydin, G.; and Qi, Z. In AGU Fall Meeting Abstracts, 2006.
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SCI: ETF Early Operations-Indiana University. Stewart, C., A.; Voss, B., D.; McRobbie, M., A.; Shankar, A.; Simms, S.; and McCaulay, D., S. Technical Report 2006.
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Navigation techniques for large-scale astronomical exploration. Fu, C.; Hanson, A., J.; and Wernert, E., A. In Proceedings of SPIE - The International Society for Optical Engineering, volume 6060, 2006.
Navigation techniques for large-scale astronomical exploration [link]Website   doi   link   bibtex   abstract  
Template-based isocontouring. Lakshmipathy, J.; Nowinski, W., L.; and Wernert, E., A. International Journal of Image and Graphics, 6(02): 187-204. 2006.
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Streaming Data Services to Support Archival and Real-Time Geographical Information System Grids. Aydin, G.; Fox, G., C.; Gadgil, H.; and Pierce, M., E. In Sixth Annual NASA Earth Science Technology Conference, 2006.
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Thin Client Collaboration Web Services. Wang, M.; Fox, G., C.; and Pierce, M. In Telecommunications, 2006. AICT-ICIW'06. International Conference on Internet and Web Applications and Services/Advanced International Conference on, pages 148, 2006.
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Integrating AJAX approach into GIS visualization web services. Sayar, A.; Pierce, M.; and Fox, G., C. In Telecommunications, 2006. AICT-ICIW'06. International Conference on Internet and Web Applications and Services/Advanced International Conference on, pages 169, 2006.
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Optimizing web service messaging performance using a context store for static data. Oh, S.; Aktas, M., S.; Pierce, M.; and Fox, G., C. In Proceedings of the 5th WSEAS international conference on Telecommunications and informatics, volume 50, pages 58, 2006.
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INTEGRATING AJAX MODELS WITH GIS VISUALIZATION WEB SERVICES. Sayar, A.; Pierce, M.; and Fox, G., C. Telecommunications, 2006. AICT-ICIW'06. International Conference on Internet and Web Applications and Services/Advanced International Conference on. 2006.
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Collaboration entities on deterministic finite automata. Wang, M.; Fox, G., C.; and Pierce, M. In Collaborative Technologies and Systems, 2006. CTS 2006. International Symposium on, pages 26-37, 2006.
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Cyberinfrastructure and Web 2.0. Pierce, M., E.; Fox, G., C.; Yuan, H.; and Deng, Y. In High Performance Computing Workshop, pages 265-287, 2006.
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XML Metadata Services and Application Usage Scenarios. Aktas, M., S.; Oh, S.; Fox, G., C.; and Pierce, M., E. In Proc. of The IEEE 2nd International Conference on Semantics, Knowledge and Grid, 2006.
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Providing Portlet-Based Client Access to CIMA-Enabled Crystallographic Instruments, Sensors, and Data. Yin, H.; Mcmullen, D., F.; Nacar, M., A.; Pierce, M.; Huffman, K.; Fox, G., C.; and Ma, Y. In Grid Computing, 7th IEEE/ACM International Conference on, pages 317-318, 2006.
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Managing Grid messaging middleware. Gadgil, H.; Fox, G., C.; Pallickara, S.; and Pierce, M. In Challenges of Large Applications in Distributed Environments, 2006 IEEE, pages 83-91, 2006.
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Building a Grid of Grids: messaging substrates and information management. Fox, G., C.; Pallickara, S.; and Pierce, M. chapter in book ``Grid Computational Methods'' Edited by MP Bekakos, GA Gravvanis and HR Arabnia. 2006.
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A retrospective on the development of web service specifications. Pallickara, S.; Aktas, M., S.; Yildiz, B.; Patel, S.; Yemme, D.; Fox, G., C.; Gadgil, H.; Pierce, M., E.; Sangyoon, O.; Oh, S.; Aktas, M., S.; Gadgil, H.; Yildiz, B.; Oh, S.; Patel, S.; Pierce, M., E.; and Yemme, D. IGI Global, 2006.
A retrospective on the development of web service specifications [link]Website   doi   link   bibtex   abstract  
A PERMIS-based Authorization Solution between Portlets and Back-end Web Services. Barahona, S., B.; Fox, G., C.; Huffman, K.; Yin, H.; Barahona, S., B.; McMullen, D., F.; Pierce, M.; Fox, G., C.; others; and Huffman, K. In International Workshop on Grid Computing Environments, 2006.
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Designing Grid Tag Libraries and Grid Beans. Nacar, M., A.; Pierce, M., E.; Erlebacher, G.; Fox, G., C.; Nacar, M., A.; and Pierce, M., E. In Second International Workshop on Grid Computing Environments GCE06 at SC06, 2006.
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Grid portal system based on GPIR. Fang, J.; Fox, G., C.; Pierce, M.; Juan, F., J., F.; Fox, G., C.; and Pierce, M. In Semantics, Knowledge and Grid, 2006. SKG'06. Second International Conference on, pages 83, 2006.
Grid portal system based on GPIR [link]Website   doi   link   bibtex   abstract  
A grid framework for visualization services in the Earth sciences. Erlebacher, G.; Yuen, D., A.; Lu, Z.; Bollig, E., F.; Pierce, M.; Pallickara, S.; Yuen, G., E., D., A.; Lu, Z.; Bollig, E., F.; Pierce, M.; and Pallickara, S. Computational Earthquake Physics: Simulations, Analysis and Infrastructure, Part II, pages 2467-2483. Birkhäuser Basel, 2006.
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Real Time Streaming Data Grid Applications. Fox, G., C.; Aktas, M., S.; Aydin, G.; Bulut, H.; Pallickara, S.; Pierce, M.; Sayar, A.; Wu, W.; and Zhai, G. Distributed Cooperative Laboratories: Networking, Instrumentation, and Measurements, pages 253-267. Springer, Boston, MA, 2006.
link   bibtex   abstract  
Grids for real time data applications. Fox, G., C.; Aktas, M., S.; Aydin, G.; Bulut, H.; Gadgil, H.; Oh, S.; Pallickara, S.; Pierce, M., E.; Sayar, A.; and Zhai, G. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 3911 LNCS: 320-332. 2006.
Grids for real time data applications [link]Website   doi   link   bibtex   abstract  
Architecture for high-performance web service communications using an information service. Oh, S.; Aktas, M., S.; Pierce, M.; and Fox, G., C. WSEAS Transactions on Computers, 5(7): 1510-1518. 2006.
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Building sensor filter grids: Information architecture for the data deluge. Fox, G., C.; Aktas, M., S.; Aydin, G.; Donnellan, A.; Gadgil, H.; Granat, R.; Pallickara, S.; Parker, J.; Pierce, M., E.; Oh, S.; Rundle, J.; Sayar, A.; and Scharber, M. In Proceedings - First International Conference on Semantics, Knowledge and Grid, SKG 2005, 2006.
Building sensor filter grids: Information architecture for the data deluge [link]Website   doi   link   bibtex   abstract  
Smart Mining of Drug Discovery Information: 1. A web service and workflow infrastructure. Dong, X.; Gilbert, K.; Guha, R.; Kim, J.; Pierce, M.; Fox, G., C.; Wild, D., J.; and others Submitted to Journal of Chemical Information and Modeling October. 2006.
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Pervasive Technology Labs Program Report, July 2007. McRobbie, M.; Adams, K.; Baker, M., P.; Fox, G., C.; Gannon, D.; Heiland, R.; Lumsdaine, A.; McMullen, D., F.; Miller, T.; Siefert-Herron, D.; Stewart, C.; and Wallace, S. Technical Report 2006.
Pervasive Technology Labs Program Report, July 2007 [link]Website   link   bibtex  
Implementing ISERVO Using Grid and GIS Services. Aktas, M.; Aydin, G.; Donnellan, A.; Fox, G., C.; Granat, R.; Grant, L.; Lyzenga, G.; McLeod, D.; Pallickara, S.; Parker, J.; and others Computational Earthquake Physics: Simulations, Analysis and ..., Part 2. 2006.
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Quakesim and the solid earth research virtual observatory. Donnellan, A.; Rundle, J.; Fox, G., C.; McLeod, D.; Grant, L.; Tullis, T.; Pierce, M.; Parker, J.; Lyzenga, G.; Granat, R.; and others Computational Earthquake Physics: Simulations, Analysis and Infrastructure, Part II, pages 2263-2279. Birkhäuser Basel, 2006.
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The Solid Earth Research Virtual Observatory: Web Services for Managing Geophysical Data and Applications. Pierce, M., E.; Fox, G., C.; Aktas, M., S.; Aydin, G.; Gadgil, H.; Qi, Z.; and Sayar, A. In PAGEOPH Special Issue for 5th ACES International Workshop., 2006.
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CINF 10-Advanced HTS data mining using web service workflows. Wild, D.; Wiggins, G.; Dong, X.; Wang, H.; Pierce, M.; Lee, J., H.; and Fox, G., C. In ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 232, 2006.
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Web Service Information Systems and Applications. Aktas, M.; Aydin, G.; Fox, G., C.; Gadgil, H.; Pierce, M., E.; and Sayar, A. In GGF-16 Global Grid Forum Semantic Grid Workshop, 2006.
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A framework for secure end-to-end delivery of messages in publish/subscribe systems. Pallickara, S.; Pierce, M.; Gadgil, H.; Fox, G., C.; Yan, Y.; and Huang, Y. In Proceedings of the 7th IEEE/ACM International Conference on Grid Computing, pages 215-222, 2006.
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The introduction of the OSCAR database API (ODA). Kim, D.; Squyres, J., M.; and Lumsdaine, A. In High-Performance Computing in an Advanced Collaborative Environment, 2006. HPCS 2006. 20th International Symposium on, pages 39, 2006. IEEE
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XML Metadata Services. Aktas, M., S.; Oh, S.; Fox, G., C.; and Pierce, M., E. In 2006 2nd International Conference on Semantics Knowledge and Grid, SKG, 2006.
XML Metadata Services [link]Website   doi   link   bibtex   abstract  
iSERVO: Implementing the international solid earth research virtual observatory by integrating computational grid and geographical information web services. Aktas, M.; Aydin, G.; Donnellan, A.; Fox, G., C.; Granat, R.; Grant, L.; Lyzenga, G.; McLeod, D.; Pallickara, S.; Parker, J.; others; Pierce, M.; Rundle, J.; Sayar, A.; and Tullis, T. Computational Earthquake Physics: Simulations, Analysis and Infrastructure, Part II, pages 2281-2296. Birkhäuser Verlag, Basel, 2006.
Computational Earthquake Physics: Simulations, Analysis and Infrastructure, Part II [link]Website   link   bibtex   abstract  
XML Metadata Services. Aktas, M., S.; Fox, G., C.; Pierce, M.; and Oh, S. Concurrency and Computation: Practice and Experience, 20(7): 801-823. 2006.
XML Metadata Services [link]Website   doi   link   bibtex   abstract  
One Teraflop Achieved with a Geographically Distributed Linux Cluster. Wang, P.; Turner, G.; Simms, S.; Hart, D.; Papakhian, M.; and Stewart, C. High-Performance Computing, pages 511-522. John Wiley & Sons, Inc., 1 2006.
High-Performance Computing [link]Website   doi   link   bibtex   abstract  
Indiana University Life Sciences Strategic Plan (Version 1.01). Indiana University Life Sciences Strategic Plan Drafting Committee Technical Report 1 2006.
Indiana University Life Sciences Strategic Plan (Version 1.01) [pdf]Paper   Indiana University Life Sciences Strategic Plan (Version 1.01) [link]Website   link   bibtex   abstract  
  2005 (87)
PViN - A scalable and flexible system for visualizing pedigree databases. Wernert, E., A.; and Lakshmipathy, J. In Proceedings of the ACM Symposium on Applied Computing, volume 1, pages 115-122, 2005.
PViN - A scalable and flexible system for visualizing pedigree databases [link]Website   doi   link   bibtex   abstract  
SNPs in the neural cell adhesion molecule 1 gene (NCAM1) may be associated with human neural tube defects. Deak, K., L.; Boyles, A., L.; Etchevers, H., C.; Melvin, E., C.; Siegel, D., G.; Graham, F., L.; Slifer, S., H.; Enterline, D., S.; George, T., M.; and Vekemans, M. Human genetics, 117(2-3): 133-142. 2005.
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MutDB services: interactive structural analysis of mutation data. Dantzer, J.; Moad, C.; Heiland, R.; and Mooney, S. Nucleic acids research, 33(suppl_2): W311-W314. 2005.
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PLATCOM: A Platform for Computational Comparative Genomics. Choi, K.; Ma, Y.; Choi, J.; and Kim, S. Bioinformatics, 21(10): 2514-2516. 2005.
PLATCOM: A Platform for Computational Comparative Genomics [link]Website   doi   link   bibtex   abstract  
A composable data management architecture for scientific applications. Ma, Y.; and Bramley, R. In Proceedings - Challenges of Large Applications in Distributed Environments, CLADE 2005, volume 2005, pages 35-44, 2005.
A composable data management architecture for scientific applications [link]Website   doi   link   bibtex   abstract  
Web Services Security and Load Balancing in Grid Environment. Fang, L.; Slominski, A.; and Gannon, D. In Proc. of International Conference on Grid Computing, Las Vegas (June 2005), 2005.
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An analysis of notification related specifications for web/grid applications. Pallickara, S.; and Fox, G., C. In Information Technology: Coding and Computing, 2005. ITCC 2005. International Conference on, volume 2, pages 762-763, 2005. IEEE
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Cooperating services for data-driven computational experimentation. Plale, B.; Gannon, D.; Huang, Y.; Kandaswamy, G.; Pallickara, S., L.; and Slominski, A. Computing in Science & Engineering, 7(5): 34-43. 2005.
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An analysis of reliable delivery specifications for Web Services. Pallickara, S.; Fox, G., C.; and Pallickara, S., L. In Information Technology: Coding and Computing, 2005. ITCC 2005. International Conference on, volume 1, pages 360-365, 2005. IEEE
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Deploying the NaradaBrokering substrate in aiding efficient web and grid service interactions. Fox, G., C.; and Pallickara, S. Proceedings of the IEEE, 93(3): 564-577. 2005.
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Towards enabling peer‐to‐peer Grids. Fox, G., C.; Pallickara, S.; and Rao, X. Concurrency and Computation: Practice and Experience, 17(7‐8): 1109-1131. 2005.
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Cost model and adaptive scheme for publish/subscribe systems on mobile grid environments. Oh, S.; Pallickara, S., L.; Ko, S.; Kim, J.; and Fox, G., C. In International Conference on Computational Science, pages 275-278, 2005. Springer
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On the discovery of brokers in distributed messaging infrastructures. Pallickara, S.; Gadgil, H.; and Fox, G., C. In Cluster Computing, 2005. IEEE International, pages 1-10, 2005. IEEE
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Cost model and adaptive scheme for publish. OH, S.; SANGMI, L., E., E., P.; KO, S.; KIM, J.; and FOX, G. Lecture notes in computer science. 2005.
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On the creation & discovery of topics in distributed publish/subscribe systems. Pallickara, S.; Fox, G., C.; and Gadgil, H. In Proceedings of the 6th IEEE/ACM International Workshop on Grid Computing, pages 25-32, 2005. IEEE Computer Society
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Service oriented architectures for science gateways on grid systems. Gannon, D.; Plale, B.; Christie, M.; Fang, L.; Huang, Y.; Jensen, S.; Kandaswamy, G.; Marru, S.; Pallickara, S.; and Shirasuna, S. Service-Oriented Computing-ICSOC 2005,21-32. 2005.
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A survey of data provenance techniques. Simmhan, Y., L.; Plale, B.; and Gannon, D. Computer Science Department, Indiana University, Bloomington IN, 47405. 2005.
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Multiscale simulations of copper electrodeposition onto a resistive substrate. Drews, T., O.; Krishnan, S.; Alameda, J., C.; Gannon, D.; Braatz, R., D.; and Alkire, R., C. IBM journal of research and development, 49(1): 49-63. 2005.
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XPOLA–An Extensible Capability-based Authorization Infrastructure for Grids. Fang, L.; Gannon, D.; and Siebenlist, F. In 4th Annual PKI R&D Workshop, pages 30-40, 2005.
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A streaming validation model for SOAP digital signature. Lu, W.; Chiu, K.; Slominski, A.; and Gannon, D. In High Performance Distributed Computing, 2005. HPDC-14. Proceedings. 14th IEEE International Symposium on, pages 243-252, 2005. IEEE
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Building applications from a web service based component architecture. Gannon, D.; Krishnan, S.; Slominski, A.; Kandaswamy, G.; and Fang, L. Component Models and Systems for Grid Applications, pages 3-17. Springer, 2005.
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Component-based software for high-performance scientific computing. Alexeev, Y.; Allan, B., A.; Armstrong, R., C.; Bernholdt, D., E.; Dahlgren, T., L.; Gannon, D.; Janssen, C., L.; Kenny, J., P.; Krishnan, M.; and Kohl, J., A. In Journal of Physics: Conference Series, volume 16, pages 536, 2005. IOP Publishing
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A generic framework for building services and scientific workflows for the grid. Kandaswamy, G.; Fang, L.; Huang, Y.; Shirasuna, S.; and Gannon, D. In Proceedings of the 2005 ACM/IEEE Conference on SuperComputing, 2005.
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Mutational spectrum of NSDHL in CHILD syndrome. Bornholdt, D.; König, A.; Happle, R.; Leveleki, L.; Bittar, M.; Danarti, R.; Vahlquist, A.; Tilgen, W.; Reinhold, U.; and Baptista, A., P. Journal of medical genetics, 42(2): e17-e17. 2005.
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A survey of data provenance in e-science. Simmhan, Y., L.; Plale, B.; and Gannon, D. ACM Sigmod Record, 34(3): 31-36. 2005.
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Towards dynamically adaptive weather analysis and forecasting in LEAD. Plale, B.; Gannon, D.; Reed, D.; Graves, S.; Droegemeier, K.; Wilhelmson, B.; and Ramamurthy, M. In International Conference on Computational Science, pages 624-631, 2005. Springer
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Service-oriented environments for dynamically interacting with mesoscale weather. Droegemeier, K., K.; Gannon, D.; Reed, D.; Plale, B.; Alameda, J.; Baltzer, T.; Brewster, K.; Clark, R.; Domenico, B.; and Graves, S. Computing in Science & Engineering, 7(6): 12-29. 2005.
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Active management of scientific data. Plale, B.; Gannon, D.; Alameda, J.; Wilhelmson, B.; Hampton, S.; Rossi, A.; and Droegemeier, K. IEEE Internet Computing, 9(1): 27-34. 2005.
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RAPID: REMOTELY ACCESSIBLE PERSONAL INFORMATION DISPLAY-BRIDGING THE GAP BETWEEN THE FIELD AND THE LABORATORY TO SYNTHESIZE ENVIRONMENTAL DATA AND FOSTER INTEGRATED AND COLLABORATIVE LEARNING. TEDESCO, L., P.; BAKER, M., P.; ROGERS, Y.; and HALL, B., E. In 2005 Salt Lake City Annual Meeting, 2005.
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Advanced Network Security Project. Wallace, S.; Travis, G.; Bates, E.; and Ripley, D. Technical Report 2005.
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On the lack of typical behavior in the global Web traffic network. Meiss, M.; Menczer, F.; and Vespignani, A. In Proceedings of the 14th international conference on World Wide Web, pages 510-518, 2005. ACM
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Worldwide Messaging Support for High Performance Real-time Collaboration. Burnap, P.; Bulut, H.; Pallickara, S.; Fox, G., C.; Walker, D.; Kaplan, A.; Yildiz, B.; and Nacar, M., A. In Proceedings of the UK e-Science All Hands Meeting, 2005.
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Performance of a possible Grid message infrastructure. Pallickara, S.; Fox, G., C.; Uyar, A.; Liu, H.; Rao, X.; Walker, D.; and Yildiz, B. Concurrency and Computation: Practice and Experience, 17(2‐4): 193-214. 2005.
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Publish/Subscribe systems on node and link error prone mobile environments. Oh, S.; Pallickara, S., L.; Ko, S.; Kim, J.; and Fox, G., C. In International Conference on Computational Science, pages 576-584, 2005. Springer
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Support for High Performance Real-time Collaboration within the NaradaBrokering Substrate. Pallickara, S.; Bulut, H.; Burnap, P.; Fox, G., C.; Uyar, A.; and Walker, D. Electrical Engineering and Computer Science. 2005.
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Monitoring access to stateful resources in grid environments. Pallickara, S., L.; Plale, B.; Jensen, S.; and Sun, Y. In Services Computing, 2005 IEEE International Conference on, volume 1, pages 343-346, 2005. IEEE
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Structure, sharing and preservation of scientific experiment data. Pallickara, S., L.; Plale, B.; Jensen, S.; and Sun, Y. In Challenges of Large Applications in Distributed Environments, 2005. CLADE 2005. Proceedings, pages 107-114, 2005. IEEE
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Vanishing Point: A Visual Road-Detection Program for a DARPA Grand Challenge Vehicle (No. TR622. Antolovic, D.; Leykin, A.; and Johnson, S., D. Indiana University. 2005.
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Asynchronous peer-to-peer web services and firewalls. Caromel, D.; Di Costanzo, A.; Gannon, D.; Slominski, A.; Di Costanzo, A.; Gannon, D.; and Caromel, D. In Parallel and Distributed Processing Symposium, 2005. Proceedings. 19th IEEE International, volume 183, pages 6-pp, 2005. IEEE
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On the costs for reliable messaging in web/grid service environments. Pallickara, S., L., S., S., L., S.; Fox, G., C.; Yildiz, B.; Patel, S.; and Yemme, D. In Proceedings of the 2005 IEEE International Conference on e-Science & Grid Computing, pages 8-pp, 2005. IEEE
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Performance of Web Services Security. Liu, H.; Pallickara, S.; Fox, G., C.; and Fox, H., L., S., P., G. Proceedings of 13th Annual Mardi Gras Conference,1-8. 2005.
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Pervasive Technology Labs Program Report, August 2005. McRobbie, M.; Adams, K.; Baker, M., P.; Fox, G., C.; Gannon, D.; Heiland, R.; Lumsdaine, A.; McMullen, D., F.; Stewart, C.; and Wallace, S. Technical Report 2005.
Pervasive Technology Labs Program Report, August 2005 [link]Website   link   bibtex  
Fault Tolerant Reliable Delivery of Events in Distributed Middleware Systems. Pallickara, S.; Fox, G., C.; and Bulut, H. In Autonomic Computing, 2004. Proceedings. International Conference on, pages 328-329, 2005. IEEE
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The john-e-box: fostering innovation, inclusion, and collaboration through accessible advanced visualization. Wernert, E.; Boyles, M.; Huffman, J., N.; Rogers, J.; Huffman, J., C.; and Stewart, C. In Proceedings of the 2005 conference on Diversity in computing (TAPIA '05), pages 64, 2005. Association for Computing Machinery (ACM)
The john-e-box: fostering innovation, inclusion, and collaboration through accessible advanced visualization [pdf]Paper   doi   link   bibtex   abstract  
Distributed Object-Based Grid Computing Environments. Haupt, T.; and Pierce, M., E. Grid Computing: Making the Global Infrastructure a Reality,713-728. 2005.
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Integrating geographical information systems and grid applications. Pierce, M.; Sayar, A.; Aydin, G.; Aktas, M.; and Gadgil, H. Technical Report Technical Report, 2005.
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Fault Tolerant Distributed Middleware for VLAB. Lu, Z.; Bollig, E., F.; Erlebacher, G.; Gardgil, H.; Yuen, D.; Pierce, M.; and Pallickara, S. In AGU Fall Meeting Abstracts, 2005.
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Dynamic Web Services for Data Analysis in the Geosciences. Erlebacher, G.; Lu, Z.; Gadgil, H.; Bollig, E., F.; Kadlec, B., J.; Yuen, D., A.; Pierce, M.; and Pallickara, S. In AGU Spring Meeting Abstracts, 2005.
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Building grid portal applications from a web service component architecture. Gannon, D.; Alameda, J.; Chipara, O.; Christie, M.; Dukle, V.; Fang, L.; Farrellee, M.; Kandaswamy, G.; Kodeboyina, D.; Krishnan, S.; and others Proceedings of the IEEE, 93(3): 551-563. 2005.
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PViN. Wernert, E., A.; and Lakshmipathy, J. In Proceedings of the 2005 ACM symposium on Applied computing - SAC '05, volume 1, pages 115, 2005. ACM Press
PViN [link]Website   doi   link   bibtex   abstract  
Grid Application Areas within DoD. Fox, G., C.; Ho, A.; and Pierce, M. Community Grids Laboratory, Indiana University, June, 7. 2005.
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Grids for the GiG and real time simulations. Fox, G., C.; Ho, A.; Pallickara, S.; Pierce, M.; and Wu, W. In Distributed Simulation and Real-Time Applications, 2005. DS-RT 2005 Proceedings. Ninth IEEE International Symposium on, pages 129-136, 2005.
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Grid-based collaboration in interactive data language applications. Wang, M.; Fox, G., C.; and Pierce, M. In Information Technology: Coding and Computing, 2005. ITCC 2005. International Conference on, volume 1, pages 335-341, 2005.
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Building problem-solving environments with application web service toolkits. Youn, C.; Pierce, M., E.; and Fox, G., C. Future Generation Computer Systems, 21(6): 856-867. 2005.
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OGC compatible geographical information systems web services. Sayar, A.; Pierce, M.; and Fox, G., C. Technical Report 2005.
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Grid Technology Overview and Status. Fox, G., C.; Ho, A.; and Pierce, M. Community Grids Lab., Indiana University, Anabas Inc. 2005.
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Appendix to Grid Technology Overview and Status for NCOW/GiG on Grid and Web Services. Fox, G., C.; Ho, A.; and Pierce, M. Distributed Simulation and Real Time Simulation. 2005.
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Managing dynamic metadata as context. Aktas, M., S.; Fox, G., C.; and Pierce, M. In The 2005 Istanbul International Computational Science and Engineering Conference (ICCSE2005), Istanbul, Turkey, 2005.
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Grid portal architectures for scientific applications. Thomas, M., P.; Burruss, J.; Cinquini, L.; Fox, G., C.; Gannon, D.; Gilbert, L.; Von Laszewski, G.; Jackson, K.; Middleton, D.; Moore, R.; and others In Journal of Physics: Conference Series, volume 16, pages 596, 2005.
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Messaging in Web service Grid with applications to geographical information systems. Fox, G., C.; Pallickara, S.; Aydin, G.; and Pierce, M. Advances in Parallel Computing, 14: 305-331. 2005.
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A scripting based architecture for management of streams and services in real-time grid applications. Gadgil, H.; Fox, G., C.; Pallickara, S.; Pierce, M.; and Granat, R. In Cluster Computing and the Grid, 2005. CCGrid 2005. IEEE International Symposium on, volume 2, pages 710-717, 2005.
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General Collaboration Structures for Interactive Data Language Applications. Wang, M.; Fox, G., C.; and Pierce, M. Electrical Engineering and Computer Science. 2005.
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Message Exchange for Web Service-Based Mapping Services. Sayar, A.; Pierce, M.; and Fox, G., C. Proceedings of GeoInformatics, 5. 2005.
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Management of real-time streaming data grid services. Fox, G., C.; Aydin, G.; Bulut, H.; Gadgil, H.; Pallickara, S.; Pierce, M.; Wu, W.; Bulut, H.; Gadgil, H.; Pallickara, S.; Pierce, M.; Wu, W.; Bulut, H.; Gadgil, H.; Pallickara, S.; Pierce, M.; and Wu, W. Grid and Cooperative Computing-GCC 2005, 19(7): 3-12. 2005.
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Instantiations of shared event model in grid-based collaboration. Wang, M.; Fox, G., C.; and Pierce, M. Electrical Engineering and Computer Science. 2005.
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Integration of Geographical Information Systems and Geophysical Applications with Distributed Computing Technologies. Pierce, M., E.; Aktas, M., S.; Aydin, G.; Fox, G., C.; Gadgil, H.; and Sayar, A. In AGU Fall Meeting Abstracts, 2005.
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An Architecture for Supporting Information in Dynamically Assembled Semantic Grids. Aktas, M., S.; Fox, G., C.; and Pierce, M. In 1st International Conference on Semantics, Knowledge and Grid, 2005.
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Developing GIS visualization web services for geophysical applications. Sayar, A.; Pierce, M.; and Fox, G., C. In ISPRS 2005 spatial data mining workshop, Ankara, Turkey, 2005.
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A Web services-based universal approach to heterogeneous fault databases. Grant, L., B.; Gould, M., M.; Donnellan, A.; McLeod, D.; Chen, A., Y.; Sung, S.; Pierce, M.; Fox, G., C.; and Rundle, P. Computing in science & engineering, 7(4): 51-57. 2005.
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Building sensor filter grids: Information architecture for the data deluge. Fox, G., C.; Aktas, M., S.; Aydin, G.; Donnellan, A.; Gadgil, H.; Granat, R.; Pallickara, S.; Parker, J.; Pierce, M., E.; Oh, S.; and others In Semantics, Knowledge and Grid, 2005. SKG'05. First International Conference on, pages 2, 2005.
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Grids for real time data applications. Fox, G., C.; Aktas, M., S.; Aydin, G.; Bulut, H.; Gadgil, H.; Oh, S.; Pallickara, S.; Pierce, M., E.; Sayar, A.; and Zhai, G. In PPAM, pages 320-332, 2005.
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VLab: A Grid for Planetary Materials Computations. da Silva, C., R.; Erlebacher, G.; Pierce, M.; Karki, B.; Yuen, D., A.; and Wentzcovitch, R., M. In AGU Fall Meeting Abstracts, 2005.
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Information Services for Grid/Web Service Oriented Architecture (SOA) Based Geospatial Applications. Aktas, M., S.; Aydin, G.; Fox, G., C.; Gadgil, H.; Pierce, M.; and Sayar, A. In Proceedings of 1st International Conference Beijing China November, pages 27-29, 2005.
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Message-based cellular peer-to-peer grids: foundations for secure federation and autonomic services. Fox, G., C.; Lim, S.; Pallickara, S.; and Pierce, M. Future Generation Computer Systems, 21(3): 401-415. 2005.
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A multi-party implementation of ws-secureconversation. Liu, H.; Fox, G., C.; Pierce, M.; and Pallickara, S. Community Grids Lab, Indiana University, Bloomington, Indiana, 47404. 2005.
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Message-Based Cellular Peer-to-Peer Grids: Foundations for Federation Security and Autonomic Services. Fox, G., C.; Lim, S.; Pallickara, S.; and Pierce, M. Future Generation Computer Systems - Special issue: P2P computing and interaction with grids, 21(3). 2005.
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Developing a Web Service-Compatible Map Server for Geophysical Applications. Sayar, A.; Aktas, M., S.; Aydin, G.; Fox, G., C.; and Pierce, M. In Submitted to ACM-GIS Conference, 2005.
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Implementing geographical information system grid services to support computational geophysics in a service-oriented environment. Aktas, M.; Aydin, G.; Donnellan, A.; Fox, G., C.; Granat, R.; Lyzenga, G.; McLeod, D.; Pallickara, S.; Parker, J.; Pierce, M.; and others In NASA Earth-Sun System Technology Conference, University of Maryland, Adelphi, Maryland, 2005.
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GridFTP and parallel TCP support in naradabrokering. Lim, S.; Fox, G., C.; Kaplan, A.; Pallickara, S.; and Pierce, M. Distributed and Parallel Computing,93-102. 2005.
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eSports: Collaborative and synchronous video annotation system in grid computing environment. Zhai, G.; Fox, G., C.; Pierce, M.; Wu, W.; and Bulut, H. In Multimedia, Seventh IEEE International Symposium on, pages 9--pp, 2005.
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SERVOGrid complexity computational environments (CCE) integrated performance analysis. Aydin, G.; Aktas, M., S.; Fox, G., C.; Gadgil, H.; Pierce, M.; and Sayar, A. In Proceedings of the 6th IEEE/ACM International Workshop on Grid Computing, pages 256-261, 2005.
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Building messaging substrates for Web and Grid applications. Fox, G., C.; Pallickara, S.; Pierce, M.; and Gadgil, H. Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 363(1833): 1757-1773. 2005.
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Revamping the OSCAR database: A flexible approach to cluster configuration data management. Kim, D.; Squyres, J., M.; and Lumsdaine, A. In High Performance Computing Systems and Applications, 2005. HPCS 2005. 19th International Symposium on, pages 326-332, 2005. IEEE
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SPECIAL THANKS TO CISE'S REVIEWERS. Angelis, L.; Batten, P.; Bell, G.; Bullock, S.; Catania, B.; Chang, P.; Chelikowsky, J.; Clarke, S.; Cuccaro, S.; Fahroo, F.; and others Computing in Science & Engineering, 7: 21. 2005.
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Information services for dynamically assembled semantic grids. Aktas, M., S.; Fox, G., C.; and Pierce, M., E. In First International Conference on Semantics, Knowledge and Grid, SKG 2005, pages 10, 2005.
Information services for dynamically assembled semantic grids [pdf]Website   doi   link   bibtex   abstract  
  2004 (45)
On the computation of (2-2) three-center Slater-type orbital integrals of l/r 12 using Fourier-transform-based analytical formulas. Antolovic, D.; and Silverstone, H., J. International Journal of Quantum Chemistry, 100(2 SPEC. ISS.): 146-154. 2004.
On the computation of (2-2) three-center Slater-type orbital integrals of l/r 12 using Fourier-transform-based analytical formulas [link]Website   doi   link   bibtex   abstract  
Building grid applications and portals: An approach based on components, web services and workflow tools. Gannon, D.; Fang, L.; Kandaswamy, G.; Kodeboyina, D.; Krishnan, S.; Plale, B.; and Slominski, A. In Euro-Par 2004 Parallel Processing, pages 1-8, 2004. Springer
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Open grid services architecture use cases. Gannon, D.; and Von Reich, J., J. Technical Report 2004.
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Toward flexible messaging for SOAP-based services. Fox, G., C.; Pallickara, S.; and Parastatidis, S. In Supercomputing, 2004. Proceedings of the ACM/IEEE SC2004 Conference, pages 8, 2004. IEEE
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A Demonstration of Collaborative Web Services and Peer-to-Peer Grids. Wang, M.; Fox, G., C.; and Pallickara, S. In ITCC (2), pages 62-67, 2004.
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On the Matching of Events in Distributed Brokering Systems. Pallickara, S.; and Fox, G., C. In ITCC (2), pages 68-76, 2004.
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Making SVG a web service in a message-based MVC architecture. Qiu, X.; Pallickara, S.; and Uyar, A. Electrical Engineering and Computer Science,122. 2004.
Making SVG a web service in a message-based MVC architecture [link]Website   link   bibtex  
Efficient Matching of Events in Distributed Middleware Systems. Pallickara, S.; and Fox, G., C. JDIM, 2(2): 79-86. 2004.
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New Tools in Education. Wang, M.; Fox, G., C.; and Pallickara, S. In CATE, pages 218-223, 2004.
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A topology viewer for distributed brokering systems. Dharurkar, A.; Pallickara, S.; and Fox, G., C. In Information Technology: Coding and Computing, 2004. Proceedings. ITCC 2004. International Conference on, volume 1, pages 228-234, 2004. IEEE
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Global multimedia collaboration system. Fox, G., C.; Wu, W.; Uyar, A.; Bulut, H.; and Pallickara, S. Concurrency and Computation: Practice and Experience, 16(5): 441-447. 2004.
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Performance comparison of security mechanisms for grid services. Shirasuna, S.; Slominski, A.; Fang, L.; and Gannon, D. In Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing, pages 360-364, 2004. IEEE Computer Society
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Checkpoint and restart for distributed components in XCAT3. Krishnan, S.; and Gannon, D. In Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing, pages 281-288, 2004. IEEE Computer Society
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Linked environments for atmospheric discovery (LEAD): A cyberinfrastructure for mesoscale meteorology research and education. Droegemeier, K., K.; Chandrasekar, V.; Clark, R.; Gannon, D.; Graves, S.; Joseph, E.; Ramamurthy, M.; Wilhelmson, R.; Brewster, K.; and Domenico, B. In 20th Conf. on Interactive Information Processing Systems for Meteorology, Oceanography, and Hydrology, 2004.
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XCAT3: A framework for CCA components as OGSA services. Krishnan, S.; and Gannon, D. In High-Level Parallel Programming Models and Supportive Environments, 2004. Proceedings. Ninth International Workshop on, pages 90-97, 2004. IEEE
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Tsunami: A high-speed rate-controlled protocol for file transfer. Meiss, M., R. Indiana University. 2004.
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Analysis of the “SQL Slammer” worm and its effects on Indiana University and related institutions. Travis, G.; Balas, E.; Ripley, D.; and Wallace, S. Technical Report 2004.
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An Efficient Scheme for Aggregation and Presentation of Network Performance. Gunduz, G.; Pallickara, S.; and Fox, G., C. Electrical Engineering and Computer Science. 2004.
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Implementing a NTP-based time service within a distributed middleware system. Bulut, H.; Pallickara, S.; and Fox, G., C. In Proceedings of the 3rd international symposium on Principles and practice of programming in Java, pages 126-134, 2004. Trinity College Dublin
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A Grid Framework for Visualization Services. Erlebacher, G.; Lu, Z.; Bollig, E., F.; Yuen, D., A.; Pierce, M.; and Pallickara, S. In AGU Fall Meeting Abstracts, 2004.
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Designing ontologies and distributed resource discovery services for an earthquake simulation grid. Aktas, M., S.; Pierce, M.; and Fox, G., F. In Proc. of the GGF11 Semantic Grid Applications Workshop, Honolulu, USA, pages 1-6, 2004.
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Gateway Portal. Pierce, M.; and Wilkerson, S. Technical Report ARMY RESEARCH LAB ABERDEEN PROVING GROUND MD COMPUTATIONAL AND INFORMATION SCIENCES, 2004.
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Bioinformatics: transforming biomedical research and medical care - Introdution. Stewart, C., A. In Communications of the ACM, volume 47, pages 30, 11 2004.
Bioinformatics: transforming biomedical research and medical care - Introdution [pdf]Paper   Bioinformatics: transforming biomedical research and medical care - Introdution [link]Website   doi   link   bibtex   abstract  
The Grid2003 production grid: principles and practice. Foster, I.; Gieraltowski, J.; Gose, S.; Maltsev, N.; May, E.; Rodriguez, A.; Sulakhe, D.; Vaniachine, A.; Green, M.; Miller, R.; Letts, J.; Martin, T.; Shank, J.; Youssef, S.; Bury, D.; Dumitrescu, C.; Engh, D.; Gardner, R.; Adams, D.; Baker, R.; Deng, W.; Smith, J.; Yu, D.; Mambelli, M.; Smirnov, Y.; Voeckler, J.; Wilde, M.; Zhao, Y.; Zhao, X.; Legrand, I.; Singh, S.; Steenberg, C.; Xia, Y.; Avery, P.; Cavanaugh, R.; Kim, B.; Prescott, C.; Rodriguez, J.; Zahn, A.; Afaq, A.; Berman, E.; Annis, J.; Bauerdick, L.; Ernst, M.; Fisk, I.; Giacchetti, L.; Graham, G.; Heavey, A.; Kaiser, J.; McKee, S.; Kuropatkin, N.; Pordes, R.; Sekhri, V.; Weigand, J.; Wu, Y.; Jordan, C.; Prewett, J.; Thomas, T.; Baker, K.; Sorrillo, L.; Severini, H.; Huth, J.; Clifford, B.; Deelman, E.; Flon, L.; Kesselman, C.; Mehta, G.; Olomu, N.; Vahi, K.; Allen, M.; Grundhoefer, L.; Hicks, J.; Luehring, F.; Peck, S.; Quick, R.; Simms, S.; De, K.; McGuigan, P.; Sosebee, M.; Fekete, G.; VandenBerg, J.; Bradley, D.; Couvares, P.; De Smet, A.; Kireyev, C.; Paulson, E.; Roy, A.; Cho, K.; Kwon, K.; Son, D.; Park, H.; Koranda, S.; Moe, B.; Canon, S.; Jackson, K.; Konerding, D.; Lee, J.; Olson, D.; Sakrejda, I.; Tierney, B.; Brown, B.; and Sheldon, P. In Proceedings. 13th IEEE International Symposium on High performance Distributed Computing (HPDC 2004), pages 236-245, 2004. IEEE
The Grid2003 production grid: principles and practice [pdf]Paper   The Grid2003 production grid: principles and practice [link]Website   doi   link   bibtex   abstract  
Making scientific applications as web services. Pierce, M.; and Fox, G., C. Computing in Science & Engineering, 6(1): 93-96. 2004.
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High performance data streaming in service architecture. Fox, G., C.; Gadgil, H.; Pallickara, S.; Pierce, M.; Grossman, R., L.; Gu, Y.; Hanley, D.; and Hong, X. Technical Report 2004.
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A Web based CCBR Recommender System for Ontology aided Metadata Discovery. Aktas, M., S.; Leake, D., B.; Pierce, M.; Fox, G., C.; and Ave, S., W. In Grid Computing, 2004. Proceedings. Fifth IEEE/ACM International Workshop on, 2004. IEEE
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A web based conversational case-based recommender system for ontology aided metadata discovery. Aktas, M., S.; Pierce, M.; Fox, G., C.; and Leake, D. In Proceedings of the 5th IEEE/ACM international workshop on grid computing, pages 69-75, 2004.
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Messaging and the Web Service Distributed Operating Environment. Fox, G., C.; Pallickara, S.; Pierce, M.; and Gadgil, H. Technical Report 2004.
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Developing a Secure Grid Computing Environment Shell Engine. Nacar, M., A.; Pierce, M.; and Fox, G., C. Neural, Parallel & Scientific Computations, 12(3): 379-390. 2004.
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iSERVO: Implementing the International Solid Earth Research Virtual Observatory. Fox, G., C.; Pierce, M.; Rundle, J.; Donnellan, A.; Parker, J.; Granat, R.; Lyzenga, G.; McLeod, D.; Grant, L.; Fox, G., C.; Granat, R.; Grant, L.; Lyzenga, G.; McLeod, D.; Pallickara, S.; Parker, J.; Pierce, M.; Rundle, J.; others; Donnellan, A.; Parker, J.; Granat, R.; Lyzenga, G.; McLeod, D.; and Grant, L. In AGU Fall Meeting Abstracts, 2004.
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Web service grids for iSERVO. Fox, G., C.; and Pierce, M. In International Workshop http://www. eps. su-tokyo. ac. jp/jp/COE21/events/20041014. pdf on Geodynamics: Observation, Modeling and Computer Simulation University of Tokyo Japan October 14 2004, 2004.
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WEB COMPUTING. Pierce, M.; and Fox, G., C. Computing in Science & Engineering, 6: 93. 2004.
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Implementing Geographic Information System Grid Services Using Distributed Messaging Systems. Pierce, M.; Fox, G., C.; and Pallickara, S. In AGU Fall Meeting Abstracts, 2004.
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Complexity Computational Environments (CCE) Architecture. Fox, G., C.; Gadgil, H.; Pallickara, S.; Pierce, M.; Rundle, J.; Donnellan, A.; Parker, J.; Granat, R.; Lyzenga, G.; McLeod, D.; and others Technical Report 2004.
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Illuminating Earth's interior through advanced computing. Donnellan, A.; Rundle, J.; Ries, J.; Fox, G., C.; Pierce, M.; Parker, J.; Crippen, R.; DeJong, E.; Chao, B.; Kuang, W.; and others Computing in Science & Engineering, 6(1): 36-44. 2004.
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QuakeTables: The Fault Database for QuakeSim. Grant, L., B.; Donnellan, A.; McLeod, D.; Pierce, M.; Chen, A., Y.; Gould, M.; Noriega-Carlos, G.; Paul, R.; Sung, S.; and Ta, M., V. In AGU Fall Meeting Abstracts, 2004.
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Complexity Computational Environment: Data Assimilation SERVOGrid. Donnellan, A.; Parker, J.; Fox, G., C.; Pierce, M.; Rundle, J.; and McLeod, D. In Proceedings of the 2004 NASA Esto Conference, 2004. Pasadena, CA: Jet Propulsion Laboratory, National Aeronautics and Space Administration, 2004.
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The QuakeSim Project: numerical simulations for active tectonic processes. Donnellan, A.; Parker, J.; Lyzenga, R.; Fox, G., C.; Pierce, M.; McLeod, D.; Grant, L.; and Tullis, T. Technical Report 2004.
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Implementing GIS Grid Services for the International Solid Earth Research Virtual Observatory. Aydin, G.; Pierce, M.; Fox, G., C.; Aktas, M.; and Sayar, A. a special issue of Pure and Applied Geophysics. 2004.
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Web Service Robust GridFTP. Lim, S.; Fox, G., C.; Pallickara, S.; and Pierce, M., E. In PDPTA, volume 4, pages 725-730, 2004.
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Management of data streams for a real time flood simulation. Gadgil, H.; Choi, J.; Engel, B.; Fox, G., C.; Ko, S.; Pallickara, S.; and Pierce, M. Technical Report 2004.
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Performance Measurements for NaradaBrokering enhanced GridFTP. Lim, S.; Fox, G., C.; Kaplan, A.; Pallickara, S.; and Pierce, M. Technical Report 2004.
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Parallel computing in biomedical research and the search for peta-scale biomedical applications. Stewart, C.; Hart, D.; Sheppard, R.; Li, H.; Cruise, R.; Moskvin, V.; and Papiez, L. Volume 13 2004.
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A novel approach to extract triangle strips for iso-surfaces in volumes. Lakshmipathy, J.; Nowinski, W., L.; and Wernert, E., A. In Proceedings of the 2004 ACM SIGGRAPH international conference on Virtual Reality continuum and its applications in industry - VRCAI '04, pages 239-245, 2004. ACM Press
A novel approach to extract triangle strips for iso-surfaces in volumes [link]Website   doi   link   bibtex   abstract  
  2003 (44)
The rationale of the current optical networking initiatives. De Laat, C.; Radius, E.; and Wallace, S. Future Generation Computer Systems, 19(6): 999-1008. 2003.
The rationale of the current optical networking initiatives [link]Website   doi   link   bibtex   abstract  
Grid Computing: Making the Global Infrastructure a Reality. Gannon, D.; Ananthakrishnan, R.; Krishnan, S.; Govindaraju, M.; Ramakrishnan, L.; and Slominski, A. Wiley, 2003.
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GRAPPA: Grid access portal for physics applications. Engh, D.; Smallen, S.; Gieraltowski, J.; Fang, L.; Gardner, R.; Gannon, D.; and Bramley, R. arXiv preprint cs/0306133. 2003.
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Building grid services for user portals. Gannon, D.; Christie, M.; Chipara, O.; Fang, L.; Farrellee, M.; Kandaswamy, G.; Lu, W.; Plale, B.; Slominski, A.; and Sarangi, A. In GGF Workshop on Designing and Building Grid Services, 2003.
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NaradaBrokering: An Event‐Based Infrastructure for Building Scalable Durable Peer‐To‐Peer Grids. Fox, G., C.; and Pallickara, S. Grid computing: making the global infrastructure a reality,579-600. 2003.
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Towards an Architecture for Audio/Video Conferencing in Distributed Brokering Systems. Uyar, A.; Pallickara, S.; and Fox, G., C. In Communications in Computing, pages 17-23, 2003.
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NaradaBrokering: a distributed middleware framework and architecture for enabling durable peer-to-peer grids. Pallickara, S.; and Fox, G., C. In Proceedings of the ACM/IFIP/USENIX 2003 International Conference on Middleware, pages 41-61, 2003. Springer-Verlag New York, Inc.
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Collaborative web services and peer-to-peer grids. Fox, G., C.; Bulut, H.; Kim, K.; Ko, S.; Lee, S.; Oh, S.; Pallickara, S.; Qiu, X.; Uyar, A.; and Wang, M. SIMULATION SERIES, 35(1): 3-12. 2003.
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A transport framework for distributed brokering systems. Pallickara, S.; Fox, G., C.; Yin, J.; Gunduz, G.; Liu, H.; Uyar, A.; and Varank, M. Electrical Engineering and Computer Science. 2003.
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A Web services framework for collaboration and videoconferencing. Fox, G., C.; Wu, W.; Uyar, A.; Bulut, H.; and Pallickara, S. In Workshop on Advanced Collaborative Environments, 2003.
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Merging the CCA component model with the OGSI framework. Govindaraju, M.; Krishnan, S.; Chiu, K.; Slominski, A.; Gannon, D.; and Bramley, R. In Cluster Computing and the Grid, 2003. Proceedings. CCGrid 2003. 3rd IEEE/ACM International Symposium on, pages 182-189, 2003. IEEE
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Performance Distributed Computing–HPDC 1999, 1999. ARMSTRONG, C., R.; GANNON, D.; GEIST, A.; KEAHEY, K.; and KOHN, S. In International Conference on Stability of Ships and Ocean Vehicles-Stab, pages 377-388, 2003.
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Web services: been there, done that?. Staab, S.; Van der Aalst, W.; Benjamins, V., R.; Sheth, A.; Miller, J., A.; Bussler, C.; Maedche, A.; Fensel, D.; and Gannon, D. IEEE Intelligent Systems, 18(1): 72-85. 2003.
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A Portal Based Approach to Viewing Aggregated Network Performance Data in Distributed Brokering Systems. Gunduz, G.; Pallickara, S.; and Fox, G., C. In International Conference on Internet Computing, pages 495-501, 2003.
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Efficient Support for Sophisticated Interactions between Entities in Distributed Brokering Systems. Pallickara, S.; and Fox, G., C. ACM Ubiquity, 4(16). 2003.
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A Distributed Collaboration Framework for Stream Annotation. Huang, T.; Pallickara, S.; and Fox, G., C. Journal of Systemics, Cybernetics, and Informatics. 2003.
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Lowering the cost of computation. Pallickara, S.; and Fox, G., C. Ubiquity, 2003(June): 1. 2003.
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A Java based web interface to MATLAB. Samsi, S.; Krishnamurthy, A.; Ahalt, S.; Nehrbass, J.; and Pierce, M. In High Performance Embedded Computing (HPEC) workshop, 2003.
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Advanced information technology support for life sciences research. Stewart, C., A.; Hart, D.; Shankar, A.; Wernert, E.; Repasky, R.; Papakhian, M.; Arenson, A., D.; and Bernbom, G. In Proceedings of the 31st annual ACM SIGUCCS conference on User services - SIGUCCS '03, pages 7-9, 2003. ACM Press
Advanced information technology support for life sciences research [pdf]Paper   Advanced information technology support for life sciences research [link]Website   doi   link   bibtex   abstract  
Interactive Poster: Tree3D–A System for Temporal and Comparative Analysis of Phylogenetic Trees. Wernert, E., A.; Berry, D., K.; Huffman, J., N.; and Stewart, C., A. POSTER COMPENDIUM,114. 2003.
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Building problem solving environments with application web service toolkits. Youn, C.; Pierce, M.; and Fox, G., C. Computational Science---ICCS 2003,717. 2003.
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Incorporating an XML Matching Engine in Distributed Brokering Systems. Pallickara, S.; Fox, G., C.; and Pierce, M., E. In PDPTA, pages 1511-1517, 2003.
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Workshop on Computational Earthquake Physics and Solid Earth System Simulation-Interacting Data Services for Distributed Earthquake Modeling. Pierce, M.; Youn, C.; and Fox, G., C. Lecture Notes in Computer Science, 2659: 863-872. 2003.
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Developing Secure Web Services for Computational Portals. Youn, C.; Pierce, M., E.; and Fox, G., C. In Security and Management, pages 367-372, 2003.
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Workshop on Complex Problem-Solving Environments for Grid Computing (WCPSE02)-Building Problem Solving Environments with Application Web Service Toolkits. Youn, C.; Pierce, M.; and Fox, G., C. Lecture Notes in Computer Science, 2660: 403-412. 2003.
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Access Control System Using Web Services for XML Messaging Systems. Kaplan, A.; Topcu, A., E.; Pierce, M., E.; and Fox, G., C. In IKE, pages 207-211, 2003.
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Interacting data services for distributed earthquake modeling. Pierce, M.; Youn, C.; and Fox, G., C. Computational Science---ICCS 2003,696. 2003.
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Implications of Grid e-Science and CyberInfrastructure for the DoD High Performance Computing Modernization Program. Fox, G., C.; and Pierce, M. Technical Report 2003.
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The international Solid Earth Virtual Research Observatory (iSERVO) institute seed project. Mora, P.; Donnellan, A.; Fox, G., C.; Pierce, M.; Matsu'Ura, M.; McLeod, D.; and Yin, X. In AGU Fall Meeting Abstracts, 2003.
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Federated Grids and their Security. Fox, G., C.; and Pierce, M. Draft 0.4, eprints. ecs. soton. ac. uk/archive. 2003.
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Scientific Applications as Web Services: A Simple Guide. Pierce, M.; and Fox, G., C. Web site: http://grids. ucs. indiana. edu/ptliupages/publications/cise_WSforeScience. pdf. 2003.
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Designing a Grid Computing Environment Shell Engine. Nacar, M., A.; Pierce, M., E.; and Fox, G., C. In International Conference on Internet Computing, pages 195-199, 2003.
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A security framework for distributed brokering systems. Pallickara, S.; Pierce, M.; Fox, G., C.; Yan, Y.; Huang, Y.; and Pallickara, S. Technical Report 2003.
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Interoperability and semantics for heterogeneous earthquake science data. Chen, A., Y.; Donnellan, A.; McLeod, D.; Fox, G., C.; Parker, J.; Rundle, J.; Grant, L.; Pierce, M.; Gould, M.; Chung, S.; and others In 2003 Semantic Web Technologies for Searching and Retrieving Scientific Data Conference, 2003.
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Online Knowledge Center Tools for Metadata Management. Aydin, G.; Altay, H.; Aktas, M., S.; Aysan, M., N.; Fox, G., C.; Ikibas, C.; Kim, J.; Kaplan, A.; Topcu, A., E.; Pierce, M.; and others In High Performance Computing Modernization Program Users Group Meeting, 2003.
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NaradaBrokering as Middleware Fabric for Grid-based Remote Visualization Services. Pallickara, S.; Erlebacher, G.; Yuen, D.; Fox, G., C.; and Pierce, M. In AGU Fall Meeting Abstracts, 2003.
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Workshop on Complex Problem-Solving Environments for Grid Computing (WCPSE02)-Automating Metadata Web Service Deployment for Problem Solving Environments. Balsoy, O.; Jin, Y.; Aydin, G.; Pierce, M.; and Fox, G., C. Lecture Notes in Computer Science, 2660: 393-402. 2003.
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Towards dependable grid and web services. Fox, G., C.; Pallickara, S.; Pierce, M.; and Walker, D. Ubiquity, 2003(August): 3. 2003.
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Automating metadata Web service deployment for problem solving environments. Balsoy, O.; Jin, Y.; Aydin, G.; Pierce, M.; and Fox, G., C. Future Generation Computer Systems, 21(6): 910-919. 2003.
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Grid portals: a scientist's access point for grid services. Gannon, D.; Fox, G., C.; Pierce, M.; Plale, B.; Von Laszewski, G.; Severance, C.; Hardin, J.; Alameda, J.; Thomas, M.; and Boisseau, J. GGF Community Practice document, working draft, 1. 2003.
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Implementing a Prototype of the Security Framework for Distributed Brokering Systems. Yan, Y.; Huang, Y.; Fox, G., C.; Pallickara, S.; Pierce, M., E.; Kaplan, A.; and Topcu, A., E. In Security and Management, pages 212-218, 2003.
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3DIVE: An immersive environment for interactive volume data exploration. Boyles, M.; and Fang, S., F. Journal of Computer Science and Technology, 18(1): 41-47. 2003.
3DIVE: An immersive environment for interactive volume data exploration [link]Website   link   bibtex   abstract  
2003 Report on Indiana University Accomplishments supported by Shared University Research Grants from IBM, Inc. Stewart, C., A.; Papakhian, M.; Hart, D.; Shankar, A.; Arenson, A.; McMullen, D., F.; Palakal, M.; Dalkilic, M.; and Ortoleva, P. Technical Report 2003.
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University Information Technology Services' Advanced IT Facilities: The least every researcher needs to know. Cruise, R.; Hart, D.; Papakhian, M.; Repasky, R.; Samuel, J.; Shankar, A.; Stewart, C., A.; and Wernert, E. Technical Report 2003.
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  2002 (34)
An authorization framework for a grid based component architecture. Ramakrishnan, L.; Rehn, H.; Alameda, J.; Ananthakrishnan, R.; Govindaraju, M.; Slominski, A.; Connelly, K.; Welch, V.; Gannon, D.; Bramley, R.; and Hampton, S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2536 LNCS: 169-180. 2002.
An authorization framework for a grid based component architecture [link]Website   link   bibtex   abstract  
iUniverse: A Collaborative Information Universe for IU. Börner, K.; Wright, E.; and Boyles, M. In Abstract submission for I-Light Conference, University Place Conference Center, Indianapolis, IN, December 4th, 2002.
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An extensible and interoperable event system architecture using SOAP. Slominski, A.; Govindaraju, M.; Gannon, D.; and Bramley, R. Department of Computer Science. 2002.
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An analysis of the open grid services architecture. Gannon, D.; Chiu, K.; Govindaraju, M.; and Slominski, A. Technical Report 2002.
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XCAT 2.0: Design and Implementation of Component based Web Services. Govindaraju, M.; Krishnan, S.; Chiu, K.; Slominski, A.; Gannon, D.; and Bramley, R. Technical Report 2002.
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JMS Compliance in the Narada Event Brokering System. Fox, G., C.; and Pallickara, S. In International Conference on Internet Computing, pages 391-402, 2002.
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Community Grids. Fox, G., C.; Balsoy, O.; Pallickara, S.; Uyar, A.; Gannon, D.; and Slominski, A. Computational Science—ICCS 2002,22-38. 2002.
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A scaleable event infrastructure for peer to peer grids. Fox, G., C.; Pallickara, S.; and Rao, X. In Proceedings of the 2002 joint ACM-ISCOPE conference on Java Grande, pages 66-75, 2002. ACM
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The Narada event brokering system: Overview and extensions. Fox, G., C.; and Pallickara, S. In Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2002.
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Integration of NaradaBrokering and Audio/Video conferencing as a web service. Bulut, H.; Fox, G., C.; Pallickara, S.; Uyar, A.; and Wu, W. Electrical Engineering and Computer Science,48. 2002.
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Programming the grid: Distributed software components, p2p and grid web services for scientific applications. Gannon, D.; Bramley, R.; Fox, G., C.; Smallen, S.; Rossi, A.; Ananthakrishnan, R.; Bertrand, F.; Chiu, K.; Farrellee, M.; and Govindaraju, M. Cluster Computing, 5(3): 325-336. 2002.
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The Proteus multiprotocol message library. Chiu, K.; Govindaraju, M.; and Gannon, D. In Supercomputing, ACM/IEEE 2002 Conference, pages 30, 2002. IEEE
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The XCAT science portal. Krishnan, S.; Bramley, R.; Gannon, D.; Ananthakrishnan, R.; Govindaraju, M.; Slominski, A.; Simmhan, Y.; Alameda, J.; Alkire, R.; and Drews, T. Scientific Programming, 10(4): 303-317. 2002.
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Toward a framework for preparing and executing adaptive grid programs. Kennedy, K.; Mazina, M.; Foster, I.; Gannon, D.; Johnsson, L.; Kesselman, C.; Aydt, R.; Reed, D.; Dongarra, J.; and Vadhiyar, S. In ipdps, pages 171, 2002. IEEE
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A summary of grid computing environments. Fox, G., C.; Gannon, D.; and Thomas, M. CONCURRENCY AND COMPUTATION, 14(13/15): 1035-1044. 2002.
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Xcat 2.0: A component-based programming model for grid web services. Govindaraju, M.; Krishnan, S.; Chiu, K.; Slominski, A.; Gannon, D.; and Bramley, R. In Submitted to Grid 2002, 3rd International Workshop on Grid Computing, 2002.
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Grid web services and application factories. Gannon, D.; Ananthakrishnan, R.; Krishnan, S.; Govindaraju, M.; Ramakrishnan, L.; and Slominski, A. Grid Computing: Making the Global Infrastructure a Reality,251-264. 2002.
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Support for peer-to-peer interactions in web brokering systems. Fox, G., C.; and Pallickara, S. ACM Ubiquity. http://grids. ucs. indiana. edu/ptliupages/projects/NaradaBrokering/papers/P2PSystems. pdf. 2002.
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Getting More for Less: A Software Distribution Model. Samuel, J., V.; Wilhite, K., J.; and Stewart, C., A. In Educause Conference in Atlanta, Georgia, 2002.
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The gateway computational web portal. Pierce, M., E.; Youn, C.; and Fox, G., C. Concurrency and Computation: Practice and Experience, 14(13-15): 1411-1426. 2002.
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Design of a Hybrid Search in the Online Knowledge Center. Kim, J.; Balsoy, O.; Pierce, M.; and Fox, G., C. In Proceedings of the IASTED International Conference on Information and Knowledge Sharing, 2002.
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The Online Knowledge Center: Building a Component Based. Balsoy, O.; Aktas, M., S.; Aydin, G.; Aysan, M., N.; Ikibas, C.; Kaplan, A.; Kim, J.; Pierce, M.; Topcu, A.; Yildiz, B.; and others In Proceedings of the International Conference on Information and Knowledge Engineering, 2002.
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Conference Papers-Grid and Applications-The Gateway Computational Web Portal: Developing Web Services for High Performance Computing. Pierce, M.; Youn, C.; and Fox, G., C. Lecture Notes in Computer Science, 2329: 503-512. 2002.
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The Solid Earth Research Virtual Observatory: A web-based system for modeling multi-scale earthquake processes. Donnellan, A.; Fox, G., C.; Rundle, J.; McLeod, D.; Tullis, T.; Grant, L.; Parker, J.; Pierce, M.; Lyzenga, G.; Chen, A.; and others In AGU Fall Meeting Abstracts, 2002.
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Interoperable Web services for computational portals. Pierce, M.; Fox, G., C.; Youn, C.; Mock, S.; Mueller, K.; and Balsoy, O. In Proceedings of the 2002 ACM/IEEE conference on Supercomputing, pages 1-12, 2002.
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An XML Based System for Dynamic Message Content Creation, Delivery, and Control. Aydin, G.; Kaplan, A.; Topcu, A., E.; Yildiz, B.; Balsoy, O.; Pierce, M.; and Fox, G., C. In Proceedings of IASTED International Conference on Information and Knowledge Sharing (IKS 2002), 2002.
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A Batch Script Generator Web Service for Computational Portals. Mock, S., A.; Youn, C.; Pierce, M., E.; Fox, G., C.; and Thomas, M. In HPDC, pages 421, 2002.
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Design Features and Technology Evaluations for the PET Online Knowledge Center. Aktas, M.; Aydin, G.; Aysan, M., N.; Balsoy, O.; Fox, G., C.; Ikibas, C.; Kaplan, A.; Kim, J.; Pierce, M.; Topcu, A.; and others Technical Report 2002.
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An Architecture for e-Science and its Implications. Fox, G., C.; Bulut, H.; Kim, K.; Ko, S.; Lee, S.; Oh, S.; Rao, X.; Pallickara, S.; Pei, Q.; Pierce, M.; and others In Proceedings of the 2002 International Symposium on Performance Evaluation of Computer and Telecommunications Systems, edited by Mohammed S. Obaidat, Franco Davoli, Ibrahim Onyuksel and Raffaele Bolla, Society for Modeling and Simulation International, pages 14-24, 2002.
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Grid services for earthquake science. Fox, G., C.; Ko, S.; Pierce, M.; Balsoy, O.; Kim, J.; Lee, S.; Kim, K.; Oh, S.; Rao, X.; Varank, M.; and others Concurrency and Computation: Practice and Experience, 14(6-7): 371-393. 2002.
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Case study: Constructing the solar journey. Hanson, A.; Fu, C.; Wernert, E.; and Frisch, P. Preprint. 2002.
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Gauging IT support strategies: User needs then and now. Samuel, J.; Peebles, C.; Noguchi, T.; and Stewart, C. In Proceedings ACM SIGUCCS User Services Conference, 2002.
link   bibtex   abstract  
INGEN's advanced IT facilities: The least you need to know. Cruise, R.; Hart, D.; Papakhian, M.; Repasky, R.; Samuel, J.; Shankar, A.; Stewart, C., A.; and Wernert, E. Technical Report 2002.
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  2001 (10)
Karma2: Provenance Management for Data Driven Workflows Extended and invited from ICWS 2006 with id 217. Simmhan, Y., L.; Plale, B.; and Gannon, D. International Journal of Web Services Research. 2001.
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Center for Component Technology for Terascale Simulation Software. SNL, R., A.; Bernholdt, D.; SNL, L., F., D.; Gannon, D.; Kohl, J.; Kumfert, G.; Nieplocha, J.; Parker, S.; Rasmussen, C.; and Armstrong, R. Technical Report 2001.
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Initial Results from an early prototype of the Grid Event Service. Pallickara, S.; and Fox, G., C. Technical Report 2001.
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A Scalable Durable Grid Event Service. Fox, G., C.; and Pallickara, S. Electrical Engineering and Computer Science,123. 2001.
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The grid event service (ges) framework: Research direction & issues. Pallickara, S.; and Fox, G., C. Technical Report 2001.
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Quantum films adsorbed on graphite: Third and fourth helium layers. Pierce, M.; and Manousakis, E. Physical Review B, 63(14): 144524. 2001.
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Parallel implementation and performance of fastDNAml. Stewart, C., A.; Hart, D.; Berry, D., K.; Olsen, G., J.; Wernert, E., A.; and Fischer, W. In Proceedings of the 2001 ACM/IEEE conference on Supercomputing (CDROM) - Supercomputing '01, pages 20-20, 2001. ACM Press
Parallel implementation and performance of fastDNAml [link]Website   doi   link   bibtex   abstract   1 download  
Measuring quality, cost, and value of IT services. Peebles, C.; Voss, B.; Stewart, C.; and Workman, S. In Proceedings of the 55th Annual Quality Congress, 2001. American Society for Quality
Measuring quality, cost, and value of IT services [link]Website   link   bibtex   abstract  
High performance computing - Delivering valuable and valued services at colleges and universities. Stewart, C., A.; Peebles, C., S.; Papakhian, M.; Samuel, J.; Hart, D.; and Simms, S. In Proceedings of the 29th annual ACM SIGUCCS conference on User services - SIGUCCS '01, pages 266, 2001. ACM Press
High performance computing - Delivering valuable and valued services at colleges and universities [pdf]Paper   High performance computing - Delivering valuable and valued services at colleges and universities [link]Website   doi   link   bibtex   abstract  
Measuring Quality, Cost, and Value of IT Services. Peebles, Christopher; Stewart, Craig; Voss, Brian; Workman, S. In EDUCAUSE Conference Proceedings, 2001. EDUCAUSE
Measuring Quality, Cost, and Value of IT Services [link]Website   link   bibtex   abstract  
  2000 (9)
Requirements for and evaluation of RMI protocols for scientific computing. Govindaraju, M.; Slominski, A.; Choppella, V.; Bramley, R.; and Gannon, D. In Supercomputing, ACM/IEEE 2000 Conference, pages 61, 2000. IEEE
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Very Large Scale Visualization Methods for Astrophysical Data. Hanson, A., J.; Fu, C.; and Wernert, E., A. In VisSym, pages 115-124, 2000. Springer
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Indiana University Shared University Research grants-Report on Accomplishments. Stewart, C., A.; Bramley, R.; Bernbom, G.; Dunn, J., W.; Meglicki, Z.; McMullen, D., F.; Hart, D.; and Papakhian, M. Technical Report 2000.
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The gateway computational web portal: Developing web services for high performance computing. Pierce, M., E.; Youn, C.; and Fox, G., C. International Conference on Computational Science,503-512. 2000.
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Role of substrate corrugation in helium monolayer solidification. Pierce, M., E.; and Manousakis, E. Physical Review B, 62(8): 5228. 2000.
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Quantum Films: Simulation of Helium on Graphite. Pierce, M.; and Manousakis, E. CONDENSED MATTER THEORIES, 15: 127-138. 2000.
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Computational Biology and High Performance Computing 2000. Simon, H., D.; Zorn, M., D.; Spengler, S., J.; Shoichet, B., K.; Stewart, C., A.; Dubchak, I., L.; and Arkin, A., P. In Computational Biology and High Performance Computing 2000, 2000.
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Tethering and reattachment in collaborative virtual environments. Wernert, E., A.; and Hanson, A., J. In Proceedings - Virtual Reality Annual International Symposium, pages 292, 2000. IEEE, Los Alamitos, CA, United States
Tethering and reattachment in collaborative virtual environments [link]Website   link   bibtex   abstract  
Research and Academic Computing Implementation Plan. Peebles, C., S.; Stewart, C., A.; Bernbom, G.; McMullen, D., F.; Shankar, A.; Samuel, J.; Daniels, J.; Papakhian, M.; Hart, D.; and Walsh, J. Technical Report 2000.
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  1999 (6)
Monolayer Solid H 4 e Clusters on Graphite. Pierce, M., E.; and Manousakis, E. Physical Review Letters, 83(25): 5314. 1999.
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Path-integral Monte Carlo studies of helium on graphite. Pierce, M., E. 1999.
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Framework for assisted exploration with collaboration. Wernert, E., A.; and Hanson, A., J. In Proceedings of the IEEE Visualization Conference, pages 241-248, 1999. IEEE, Los Alamitos, CA, United States
Framework for assisted exploration with collaboration [link]Website   link   bibtex   abstract  
A constrained navigation framework for individual and exploration of 3d environmentscollaborative. Wernert, E., A. In Visualization '99, 1999. Indiana University
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Evolutionary biology and computational grids. Stewart, C., A.; Tan, T., W.; Buckhorn, M.; Hart, D.; Berry, D., K.; Zhang, L.; Wernert, E.; Sakharkar, M.; Fischer, W.; and McMullen, D., F. In CASCON Workshop on Computational Biology, 1999.
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Datasets Published by the IU Pervasive Technology Institute. Stewart, C., A.; Plale, B.; and Fischer, J. Technical Report 8 1999.
Datasets Published by the IU Pervasive Technology Institute [pdf]Paper   Datasets Published by the IU Pervasive Technology Institute [link]Website   link   bibtex   abstract  
  1998 (1)
Developing and Evaluating Abstractions for Distributed Supercomputing. Gannon, K., K., D. Cluster Computing, 1: 69-79. 1998.
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  undefined (3)
ÐÔ: An Integrated Language-Directed Performance Prediction Åeasurement and Analysis Environment. Reed, D., A.; Padua, D., A.; Foster, I., T.; Gannon, D., B.; and Miller, B., P. Technical Report .
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Towards a high performance virtualized iaas deployment. Younge, A., J.; Walters, J., P.; Suh, J.; Kang, D., D.; Park, Y.; Crago, S., P.; and Fox, G., C. . .
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FutureGrid Image Management Framework to Support Cloud and HPC Dynamic Provisioning. Diaz, J.; von Laszewski, G.; Wang, F.; and Fox, G., C. . .
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