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  2020 (5)
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 [link]Website   doi   link   bibtex   abstract   1 download  
Explore True Performance Using Application Benchmark for the Next Generation HPC Systems. Henschel, R.; Li, J.; Eigenmann, R.; and Chandrasekaran, S. Technical Report Indiana University, 2020.
Explore True Performance Using Application Benchmark for the Next Generation HPC Systems [link]Website   link   bibtex  
Image Archives Made Easy with Docker and ImageX. Young, M., D.; Gopu, A.; Perigo, R.; and Hayashi, S. ASPC, 522: 267. 2020.
link   bibtex   abstract  
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. . 2020.
Indiana University Pervasive Technology Institute preproposal and proposal management, documentation, and templates [link]Website   link   bibtex   abstract   3 downloads  
  2019 (20)
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 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  
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  
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   1 download  
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  
Beyond Campus Bridging. 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), pages 1-4, 7 2019. ACM
Beyond Campus Bridging [link]Website   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 [link]Website   doi   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 [link]Website   doi   link   bibtex   abstract  
Assessment of non-financial returns on cyberinfrastructure. Stewart, C., A.; Slavin, S., D.; Apon, A.; Hancock, D., Y.; Furlani, T.; Sill, A.; Wernert, J.; Lifka, D.; Berente, N.; and Cheatham, T. 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  
Extending XSEDE Innovations to Campus Cyberinfrastructure-The XSEDE National Integration Toolkit 1 INTRODUCTION 1.1 Overview of XCRI. Coulter, E.; Sprouse, J.; Reynolds, R.; and Knepper, R. Journal of Computational Science Education, 10(1): 16-20. 2019.
Extending XSEDE Innovations to Campus Cyberinfrastructure-The XSEDE National Integration Toolkit 1 INTRODUCTION 1.1 Overview of XCRI [pdf]Paper   Extending XSEDE Innovations to Campus Cyberinfrastructure-The XSEDE National Integration Toolkit 1 INTRODUCTION 1.1 Overview of XCRI [link]Website   doi   link   bibtex   abstract  
ABI Sustaining: The National Center for Genome Analysis Support 2019 Annual Report. Doak, T., G.; Stewart, C., A.; Hahn, R.; and Yuzhen, M. Technical Report 2019.
ABI Sustaining: The National Center for Genome Analysis Support 2019 Annual Report [pdf]Paper   ABI Sustaining: The National Center for Genome Analysis Support 2019 Annual Report [link]Website   link   bibtex  
Jetstream NSF Annual Report. Hancock, D., Y.; Fischer, J.; Taylor, J.; Snapp-childs, W.; and Vaughn, M. Technical Report 2019.
Jetstream NSF Annual Report [link]Website   link   bibtex  
Annual User Assessment - 2019 Summary Report. Hancock, D., Y.; Snapp-childs, W.; Wernert, J.; and Jankowski, H., E. Technical Report 2019.
Annual User Assessment - 2019 Summary Report [link]Website   link   bibtex  
Performance Characteristics of Virtualized GPUs for Deep Learning. Michael, S.; Teige, S.; Li, J.; Lowe, J., M.; Turner, G.; and Henschel, R. 2019.
Performance Characteristics of Virtualized GPUs for Deep Learning [link]Website   link   bibtex  
A 3D hydrodynamics study of gravitational instabilities in a young circumbinary disc. Desai, K., M.; Steiman-Cameron, T., Y.; Michael, S.; Cai, K.; and Durisen, R., H. Monthly Notices of the Royal Astronomical Society, 483(2): 2347-2361. 2019.
doi   link   bibtex   abstract  
Research Computing Desktops: Demystifying research computing for non-Linux users. Thota, A.; Weakley, L., M.; Fulton, B.; Dennis, H., E., C., B.; Huber, L.; Michael, S.; Snapp‐Childs, W.; Harrell, S., L.; Younts, A.; Dietz, D., T.; Phillips, C.; and Zhu, X. PEARC19: Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning),1-8. 2019.
link   bibtex  
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 (15)
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 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  
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  
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  
Grid Technology for Supporting Health Education and Measuring the Health Outcome. Sukhija, N.; Datta, A., K.; Sevin, S.; and Coulter, E. In Proceedings of the Practice and Experience on Advanced Research Computing, of PEARC '18, pages 89:1--89:4, 2018. ACM
Grid Technology for Supporting Health Education and Measuring the Health Outcome [link]Website   doi   link   bibtex  
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  
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.; 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   1 download  
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  
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
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  
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  
ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report. Michaels, S., D.; 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  
  2017 (24)
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  
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  
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.
link   bibtex  
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.
link   bibtex  
Summary of the 2017 NCGAS User Survey. Doak, T., G.; Stewart, C., A.; and Michaels, S., D. Technical Report 2017.
link   bibtex  
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  
Indiana University Pervasive Technology Institute. Stewart, C., A.; Welch, V.; Plale, B.; Fox, G.; Pierce, M.; and Sterling, T. Technical Report 2017.
doi   link   bibtex  
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  
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  
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.
doi   link   bibtex   abstract  
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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Using the Jetstream Research Cloud to provide Science Gateway resources. Knepper, R.; Coulter, E.; Pierce, M.; Marru, S.; and Pamidighantam, S. 2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID),753-757. 5 2017.
Using the Jetstream Research Cloud to provide Science Gateway resources [link]Website   doi   link   bibtex  
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  
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  
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  
Jetstream. Fischer, J.; Hancock, D., Y.; Lowe, J., M.; Turner, G.; Snapp-Childs, W.; and Stewart, C., A. In Proceedings of the 2017 ACM Annual Conference on SIGUCCS - SIGUCCS '17, volume Part F1317, pages 67-72, 10 2017. ACM Press
Jetstream [pdf]Paper   Jetstream [link]Website   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 IEEE International Conference on Cloud Computing, CLOUD, volume 2017-June, pages 82-89, 9 2017. IEEE Computer Society
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) [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 [link]Website   link   bibtex  
  2016 (19)
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.
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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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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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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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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  
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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Cyberinfrastructure as a platform to facilitate effective collaboration between institutions and support collaboratories. Coulter, E.; Knepper, R.; Pierce, M.; Fischer, J.; Lifka, D.; Stewart, C.; Hallock, B.; and Navarro, J. In Proceedings ACM SIGUCCS User Services Conference, volume 06-09-Nove, 2016.
doi   link   bibtex   abstract  
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  
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 Conference on Diversity, Big Data, and Science at Scale (XSEDE16), volume 17-21-July, 2016. ACM Press, New York
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  
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  
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  
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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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.
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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  
Jetstream. Stewart, C., A.; Stanzione, D., C.; Taylor, J.; Skidmore, E.; Hancock, D., Y.; Vaughn, M.; Fischer, J.; Cockerill, T.; Liming, L.; Merchant, N.; Miller, T.; and Lowe, J., M. In Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, volume 17-21-July, pages 1-8, 7 2016. ACM Press
Jetstream [pdf]Paper   Jetstream [link]Website   doi   link   bibtex   abstract  
  2015 (26)
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  
UITS Research Technologies update. Stewart, C., A. Technical Report 2015.
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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  
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.
Research proposal: Barriers to new user and new domain adoption of the XSEDE cyberinfrastructure [link]Website   doi   link   bibtex   abstract  
Performance Optimization for the Trinity RNA-Seq Assembler. Wagner, M.; Fulton, B.; and Henschel, R. Tools for High Performance Computing. 2015.
Performance Optimization for the Trinity RNA-Seq Assembler [link]Website   link   bibtex   abstract  
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  
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.
SPEC ACCEL: A standard application suite for measuring hardware accelerator performance [link]Website   doi   link   bibtex   abstract  
Cyberinfrastructure Begins at Home. Hancock, D., Y.; Henschel, R.; Kallback-Rose, K.; and Stewart, C., A. In SPXXL Winter Workshop, 2015.
Cyberinfrastructure Begins at Home [link]Website   link   bibtex   abstract  
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  
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
Facilitating scientific collaborations by delegating identity management: Reducing barriers & roadmap for incremental implementation [link]Website   doi   link   bibtex   abstract  
IU PTI/UITS Research Technologies Annual Report: FY 2014. Stewart, C., A.; and Miller, T. Technical Report 2015.
link   bibtex  
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
Programmable Immersive Peripheral Environmental System (PIPES): A prototype control system for environmental feedback devices [link]Website   doi   link   bibtex   abstract  
Scalability testing of dne2 in lustre 2.7. Crowe, T.; Lavender, N.; and Simms, S. Lustre Users Group. 2015.
link   bibtex  
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.
Workshop Report: Campus Bridging: Reducing Obstacles on the Path to Big Answers 2015 [link]Website   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
XCBC and XNIT - Tools for Cluster Implementation and Management in Research and Training [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  
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
Jetstream: A Distributed Cloud Infrastructure for Under Resourced Higher Education Communities [pdf]Paper   Jetstream: A Distributed Cloud Infrastructure for Under Resourced Higher Education Communities [link]Website   doi   link   bibtex   abstract  
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.
Building a Chemical-Protein Interactome on the Open Science Grid [pdf]Website   doi   link   bibtex   abstract  
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  
Pervasive Technology Institute annual report: Research innovations and advanced cyberinfrastructure services in support of IU strategic goals during FY 2015. Stewart, Craig A.; Plale, Beth; Welch, Von; Link, Matthew R.; Miller, Therese; Wernert, Eric A.; Boyles, Michael J.; Fulton, Ben; Hancock, David Y.; Henschel, Robert; Michael, Scott A.; Pierce, Marlon; Ping, Robert J.; Gniady, Tassie; Fox, Geoffrey C.; Mi, G. Technical Report 2015.
Pervasive Technology Institute annual report: Research innovations and advanced cyberinfrastructure services in support of IU strategic goals during FY 2015 [pdf]Paper   Pervasive Technology Institute annual report: Research innovations and advanced cyberinfrastructure services in support of IU strategic goals during FY 2015 [link]Website   link   bibtex  
  2014 (23)
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  
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  
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  
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  
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  
Models for Sustainability for Robust Cyberinfrastructure Software-Software Sustainability Survey. Wernert, J.; Wernert, E.; and Stewart, C. Technical Report 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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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  
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  
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  
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  
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  
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  
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  
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  
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  
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  
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.
link   bibtex  
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 [link]Website   link   bibtex  
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 [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 (19)
Visual exploration and analysis of human-robot interaction rules. Zhang, H.; and Boyles, M. 2013.
Visual exploration and analysis of human-robot interaction rules [link]Website   link   bibtex  
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  
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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Identity management for virtual organizations: An experience-based model. Cowles, R.; Jackson, C.; and Welch, V. In Proceedings - IEEE 9th International Conference on e-Science, e-Science 2013, pages 278-284, 2013. IEEE Computer Society
Identity management for virtual organizations: An experience-based model [link]Website   doi   link   bibtex   abstract  
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. ACM Press
XSEDE-enabled high-throughput lesion activity assessment [link]Website   doi   link   bibtex  
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  
Discipline Categories (for Cyberinfrastructure) at Indiana University. Stewart, C., A. Technical Report 2013.
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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  
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.
link   bibtex  
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  
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  
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.
Performance and quality of service of data and video movement over a 100 Gbps testbed [pdf]Paper   Performance and quality of service of data and video movement over a 100 Gbps testbed [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 [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) [link]Website   link   bibtex   abstract  
  2012 (27)
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  
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  
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  
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  
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  
48 Month Program Report. McRobbie, M., A.; Wheeler, B., C.; Plale, B., A.; and Stewart, C., A. Technical Report 2012.
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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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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  
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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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  
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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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.
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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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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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.
doi   link   bibtex   abstract  
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  
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.
doi   link   bibtex   abstract  
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  
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 ACM International Conference Proceeding SeriesProceedings 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  
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  
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.
2012 Annual Report - Advanced Biomedical Information Technology Core [link]Website   link   bibtex  
  2011 (20)
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  
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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A roadmap for using NSF cyberinfrastructure with InCommon. Welch, V.; Walsh, A.; Barnett, W.; 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  
A Roadmap for Using NSF Cyberinfrastructure with InCommon: Abbreviated Version. Barnett, W.; Welch, V.; Walsh, A.; and Stewart, C., A. Technical Report 2011.
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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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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  
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  
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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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  
Campus Bridging: Data and Networking Issues Workshop Report. Almes, G., T.; Jent, D.; and Stewart, C., A. Technical Report 2011.
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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  
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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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  
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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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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Campus Bridging Birds-of-a-Feather Session at TeraGrid 2011 Conference. Knepper, R.; and Stewart, C., A. Technical Report 2011.
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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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A roadmap for using NSF cyberinfrastructure with InCommon. Barnett, W.; Welch, V.; Walsh, A.; and Stewart, C., A. Technical Report 2011.
A roadmap for using NSF cyberinfrastructure with InCommon [link]Website   link   bibtex  
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  
  2010 (14)
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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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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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  
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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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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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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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  
Progress Report on Implementation of Recommendations from the Indiana University Cyberinfrastructure Research Taskforce. Stewart, C., A. Technical Report 2010.
Progress Report on Implementation of Recommendations from the Indiana University Cyberinfrastructure Research Taskforce [link]Website   link   bibtex   abstract  
  2009 (14)
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.
Virtual simulation for lighting and design education [link]Website   doi   link   bibtex   abstract  
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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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
Virtual reality technology and the teaching of architectural lighting [link]Website   link   bibtex   abstract  
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.
Where information searches for you: The visible past ubiquitous knowledge environment for digital humanities [link]Website   doi   link   bibtex   abstract  
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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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
GeneIndex: An Open Source Parallel Program for Enumerating and Locating Words in a Genome [link]Website   doi   link   bibtex   abstract  
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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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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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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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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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
MyOSG [link]Website   doi   link   bibtex   abstract  
  2008 (4)
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  
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  
Cyberinfrastructure resources for U.S. scholarship - The TeraGrid. Simms, S.; Stewart, C.; and McCaulay, S. In Proceedings ACM SIGUCCS User Services Conference, 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  
  2007 (9)
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  
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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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  
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  
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  
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  
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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Report of the Indiana University Research Data Management Taskforce. Technical Report 2007.
Report of the Indiana University Research Data Management Taskforce [link]Website   link   bibtex   abstract  
  2006 (8)
Progress towards petascale applications in biology: Status in 2006. Stewart, C., A.; Müller, M., S.; and Lingwall, M. In Euro-Par 2006 Workshops, pages 289-303, 2006. Springer
Progress towards petascale applications in biology: Status in 2006 [link]Website   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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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  
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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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) [link]Website   link   bibtex   abstract  
  2005 (3)
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  
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  
  2004 (5)
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  
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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Bioinformatics: transforming biomedical research and medical care. Stewart, C., A. Communications of the ACM, 47(11): 30. 11 2004.
Bioinformatics: transforming biomedical research and medical care [pdf]Paper   Bioinformatics: transforming biomedical research and medical care [link]Website   doi   link   bibtex  
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  
A global grid for analysis of arthropod evolution. Stewart, C., A.; Keller, R.; Repasky, R.; Hess, M.; Hart, D.; Müller, M.; Sheppard, R.; Wössner, U.; Aumüller, M.; Li, H.; Berry, D., K.; and Colbourne, J. In Proceedings - IEEE/ACM International Workshop on Grid Computing, pages 328-337, 2004.
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  2003 (5)
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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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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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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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  
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  
  2002 (5)
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.
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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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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 (4)
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. Technical Report 2001.
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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, 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  
  2000 (5)
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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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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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  
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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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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  1999 (4)
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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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  
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 [link]Website   link   bibtex   abstract  
  undefined (2)
Technical Report: XSEDE Return on Investment (Proxy) Data and Analysis Methods, July 2014 to August 2019.
Technical Report: XSEDE Return on Investment (Proxy) Data and Analysis Methods, July 2014 to August 2019 [link]Website   link   bibtex  
Indiana University Pervasive Technology Institute preproposal and proposal management, documentation, and templates.
Indiana University Pervasive Technology Institute preproposal and proposal management, documentation, and templates [link]Website   link   bibtex