2018 (4)
Semantic Software Metadata for Workflow Exploration and Evolution. Carvalho, L.; Garijo, D.; Medeiros, C. B.; and Gil, Y. In Proceedings of the Fourteenth IEEE International Conference on eScience, Amsterdam, The Netherlands, 2018.
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P4ML: A Phased Performance-Based Pipeline Planner for Automated Machine Learning. Gil, Y.; Yao, K.; Ratnakar, V.; Garijo, D.; Steeg, G. V.; Szekely, P.; Brekelmans, R.; Kejriwal, M.; Luo, F.; and Huang, I. In Proceedings of Machine Learning Research, ICML 2018 AutoML Workshop, 2018.
P4ML: A Phased Performance-Based Pipeline Planner for Automated Machine Learning [pdf]Paper   bibtex
MINT: Model Integration Through Knowledge-Powered Data and Process Composition. Gil, Y.; Cobourn, K.; Deelman, E.; Duffy, C.; da Silva, R. F.; Kemanian, A.; Knoblock, C.; Kumar, V.; Peckham, S.; Carvalho, L.; Chiang, Y.; Garijo, D.; Khider, D.; Khandelwal, A.; Pahm, M.; Pujara, J.; Ratnakar, V.; Stoica, M.; and Vu, B. In Proceedings of the Ninth International Congress on Environmental Modeling and Software, Ft Collins, CO, 2018.
MINT: Model Integration Through Knowledge-Powered Data and Process Composition [pdf]Paper   bibtex
Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution. da Silva, R. F.; Garijo, D.; Peckham, S. D.; Gil, Y.; Deelman, E.; and Ratnakar, V. In Proceedings of the Ninth International Congress on Environmental Modeling and Software, Ft Collins, CO, 2018.
Towards Model Integration via Abductive Workflow Composition and Multi-Method Scalable Model Execution [pdf]Paper   bibtex
  2017 (7)
NiW: Converting Notebooks into Workflows to Capture Dataflow and Provenance. Carvalho, L. A. M. C.; Wang, R.; Gil, Y.; and Garijo, D. In Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP), Austin, Texas, 2017.
NiW: Converting Notebooks into Workflows to Capture Dataflow and Provenance [link]Paper   bibtex
Requirements for Supporting the Iterative Exploration of Scientific Workflow Variants. Carvalho, L. A. M. C.; Essawy, B. T.; Garijo, D.; Medeiros, C. B.; and Gil, Y. In Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP), Austin, Texas, 2017.
Requirements for Supporting the Iterative Exploration of Scientific Workflow Variants [link]Paper   bibtex
Improving Publication and Reproducibility of Computational Experiments through Workflow Abstractions. Gil, Y.; Garijo, D.; Knoblock, M.; Deng, A.; Adusumilli, R.; Ratnakar, V.; and Mallick, P. In Proceedings of the Workshop on Capturing Scientific Knowledge (SciKnow), held in conjunction with the ACM International Conference on Knowledge Capture (K-CAP), Austin, Texas, 2017.
Improving Publication and Reproducibility of Computational Experiments through Workflow Abstractions [link]Paper   bibtex
Scientific Workflows in Data Analysis: Bridging Expertise Across Multiple Domains. Sethi, R.; and Gil, Y. Future Generation Computer Systems, 75. 2017.
Scientific Workflows in Data Analysis: Bridging Expertise Across Multiple Domains [link]Link   doi   bibtex
Abstract, Link, Publish, Exploit: An End to End Framework for Workflow Sharing. Garijo, D.; Gil, Y.; and Corcho, O. Future Generation Computer Systems, 75. 2017.
Abstract, Link, Publish, Exploit: An End to End Framework for Workflow Sharing [pdf]Paper   Abstract, Link, Publish, Exploit: An End to End Framework for Workflow Sharing [link]Link   doi   bibtex
Towards Automating Data Narratives. Gil, Y.; and Garijo, D. In Proceedings of the Twenty-Second ACM International Conference on Intelligent User Interfaces (IUI-17), Limassol, Cyprus, 2017.
Towards Automating Data Narratives [link]Paper   Towards Automating Data Narratives [link]Link   doi   bibtex
Towards Continuous Scientific Data Analysis and Hypothesis Evolution. Gil, Y.; Garijo, D.; Ratnakar, V.; Mayani, R.; Adusumilli, R.; Boyce, H.; Srivastava, A.; and Mallick, P. In Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence (AAAI-17), San Francisco, CA, 2017.
Towards Continuous Scientific Data Analysis and Hypothesis Evolution [link]Paper   bibtex
  2016 (5)
Enhancing Reproducibility for Computational Methods. Stodden, V.; McNutt, M.; Bailey, D. H.; Deelman, E.; Gil, Y.; Hanson, B.; Heroux, M. A.; Ioannidis, J. P.; and Taufer, M. Science, 354. 2016.
Enhancing Reproducibility for Computational Methods [link]Link   doi   bibtex
Reproducibility in Computer Vision: Towards Open Publication of Image Analysis Experiments as Semantic Workflows. Sethi, R. J.; and Gil, Y. In Proceedings of the Twelfth IEEE Conference on eScience, Baltimore, MD, 2016.
Reproducibility in Computer Vision: Towards Open Publication of Image Analysis Experiments as Semantic Workflows [link]Link   Reproducibility in Computer Vision: Towards Open Publication of Image Analysis Experiments as Semantic Workflows [link]Paper   doi   bibtex
Automated Hypothesis Testing with Large Scientific Data Repositories. Gil, Y.; Garijo, D.; Ratnakar, V.; Mayani, R.; Adusumilli, R.; Boyce, H.; and Mallick, P. In Proceedings of the Fourth Annual Conference on Advances in Cognitive Systems (ACS), Evanston, IL, 2016.
Automated Hypothesis Testing with Large Scientific Data Repositories [link]Paper   bibtex
Teaching Big Data Analytics Skills with Intelligent Workflow Systems. Gil, Y. In Proceedings of the Sixth Symposium on Educational Advances in Artificial Intelligence (EAAI), colocated with the National Conference of the Association for the Advancement of Artificial Intelligence (AAAI), Phoenix, AZ, 2016.
Teaching Big Data Analytics Skills with Intelligent Workflow Systems [link]Paper   bibtex
Dynamically Generated Metadata and Replanning by Interleaving Workflow Generation and Execution. Gil, Y.; and Ratnakar, V. In Proceedings of the Tenth IEEE International Conference on Semantic Computing (ICSC), Irvine, CA, 2016.
Dynamically Generated Metadata and Replanning by Interleaving Workflow Generation and Execution [link]Link   Dynamically Generated Metadata and Replanning by Interleaving Workflow Generation and Execution [link]Paper   doi   bibtex
  2015 (1)
Use of Semantic Workflows to Enhance Transparency and Reproducibility in Clinical Omics. Zheng, C. L; Ratnakar, V.; Gil, Y.; and McWeeney, S. K Genome Medicine, 7(73). 2015.
Use of Semantic Workflows to Enhance Transparency and Reproducibility in Clinical Omics [link]Paper   Use of Semantic Workflows to Enhance Transparency and Reproducibility in Clinical Omics [link]Link   doi   bibtex
  2014 (6)
Teaching Parallelism Without Programming: A Data Science Curriculum for Non-CS Students. Gil, Y. In Proceedings of the Workshop on Education for High-Performance Computing (EduHPC), held in conjunction with the IEEE ACM International Conference on High Performance Computing (SC), New Orleans, LA, 2014.
Teaching Parallelism Without Programming: A Data Science Curriculum for Non-CS Students [link]Paper   bibtex
Towards Workflow Ecosystems Through Semantic and Standard Representations. Garijo, D.; Gil, Y.; and Corcho, O. In Proceedings of the Ninth Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with the IEEE ACM International Conference on High-Performance Computing (SC), New Orleans, LA, 2014.
Towards Workflow Ecosystems Through Semantic and Standard Representations [pdf]Paper   bibtex
Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users . Garijo, D.; Corcho, O.; Gil, Y.; Braskie, M. N.; Hibar, D.; Hua, X.; Jahanshad, N.; Thompson, P.; and Toga, A. W. In Proceedings of the IEEE Conference on e-Science, Guarujua, Brazil, 2014.
Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users  [link]Link   Workflow Reuse in Practice: A Study of Neuroimaging Pipeline Users  [pdf]Paper   doi   bibtex
FragFlow: Automated Fragment Detection in Scientific Workflows . Garijo, D.; Corcho, O.; Gil, Y.; Gutman, B. A.; Dinov, I. D.; Thompson, P.; and Toga, A. W. In Proceedings of the IEEE Conference on e-Science, Guarujua, Brazil, 2014.
FragFlow: Automated Fragment Detection in Scientific Workflows  [link]Link   FragFlow: Automated Fragment Detection in Scientific Workflows  [pdf]Paper   doi   bibtex   13 downloads
Intelligent Workflow Systems and Provenance-Aware Software. Gil, Y. In Proceedings of the Seventh International Congress on Environmental Modeling and Software, San Diego, CA, 2014.
Intelligent Workflow Systems and Provenance-Aware Software [link]Paper   Intelligent Workflow Systems and Provenance-Aware Software [pdf]Link   bibtex   44 downloads
Similarity Assessment and Efficient Retrieval of Semantic Workflows. Bergmann, R.; and Gil, Y. Information Systems Journal, 40. 2014.
Similarity Assessment and Efficient Retrieval of Semantic Workflows [pdf]Paper   Similarity Assessment and Efficient Retrieval of Semantic Workflows [link]Link   bibtex   25 downloads
  2013 (11)
Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome. Garijo, D.; Kinnings, S.; Xie, L.; Xie, L.; Zhang, Y.; Bourne, P. E.; and Gil, Y. PLOS ONE. 2013.
Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome [link]Link   bibtex   21 downloads
Time-Bound Analytic Tasks on Large Datasets through Dynamic Configuration of Workflows. Gil, Y.; Ratnakar, V.; Verma, R.; Hart, A.; Ramirez, P.; Mattmann, C.; Sumarlidason, A.; and Park, S. L. In Proceedings of the Eighth Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with SC 2013, Denver, CO, 2013.
Time-Bound Analytic Tasks on Large Datasets through Dynamic Configuration of Workflows [pdf]Paper   bibtex   10 downloads
Capturing Data Analysis Expertise with Visualization in Workflows. Kale, D.; Di, S.; Liu, Y.; and Gil, Y. In AAAI Fall Symposium on Discovery Informatics: AI Takes a Science-Centered View on Big Data, Arlington, Virginia, 2013.
Capturing Data Analysis Expertise with Visualization in Workflows [pdf]Paper   bibtex   10 downloads
Common Motifs in Scientific Workflows: An Empirical Analysis. Garijo, D.; Alper, P.; Belhajjame, K.; Corcho, O.; Gil, Y.; and Goble, C. Future Generation Computer Systems. 2013.
Common Motifs in Scientific Workflows: An Empirical Analysis [link]Link   bibtex   7 downloads
Large-Scale Multimedia Content Analysis Using Scientific Workflows. Sethi, R. J.; Gil, Y.; Jo, H.; and Philpot, A. In Twenty-First ACM International Conference on Multimedia, Barcelona, Spain, 2013.
Large-Scale Multimedia Content Analysis Using Scientific Workflows [pdf]Paper   bibtex   7 downloads
Structured Analysis of the ISI Atomic Pair Actions Dataset Using Workflows. Sethi, R. J.; Jo, H.; and Gil, Y. Pattern Recognition Letters, 34(15). 2013.
Structured Analysis of the ISI Atomic Pair Actions Dataset Using Workflows [link]Link   bibtex   6 downloads
Mapping Semantic Workflows to Alternative Workflow Execution Engines. Gil, Y. In Seventh IEEE International Conference on Semantic Computing (ICSC), Irvine, CA, 2013.
Mapping Semantic Workflows to Alternative Workflow Execution Engines [pdf]Paper   bibtex   6 downloads
Detecting Common Scientific Workflow Fragments Using Templates and Execution Provenance. Garijo, D.; Corcho, O.; and Gil, Y. In Seventh ACM International Conference on Knowledge Capture (K-CAP), Banff, Canada, 2013.
Detecting Common Scientific Workflow Fragments Using Templates and Execution Provenance [pdf]Paper   bibtex   3 downloads
Using Semantic Workflows to Disseminate Best Practices and Accelerate Discoveries in Multi-Omic Data Analysis. Gil, Y.; McWeeney, S.; and Mason, C. E. In AAAI Workshop on Expanding the Boundaries of Health Informatics using AI (HIAI), held in conjunction with the Conference of the Association for the Advancement of Artificial Intelligence (AAAI), Bellevue, WA, 2013.
Using Semantic Workflows to Disseminate Best Practices and Accelerate Discoveries in Multi-Omic Data Analysis [pdf]Paper   bibtex   10 downloads
Intelligent Assistance to Disseminate Best Practices and Accelerate Discoveries in Cancer Omics. Gil, Y.; Mason, C. E.; Zheng, C.; and McWeeney, S. 2013. 2013 NCI EDRN Cancer Biomarkers Bioinformatics Workshop, Pasadena, CA
Intelligent Assistance to Disseminate Best Practices and Accelerate Discoveries in Cancer Omics [pdf]Paper   bibtex   1 download
Towards Task-Centered Network Models through Semantic Workflows. Gil, Y. In Proceedings of the IEEE Conference on Intelligence and Security Informatics (ISI), Seattle, WA, 2013.
Towards Task-Centered Network Models through Semantic Workflows [pdf]Paper   bibtex   8 downloads
  2012 (5)
Scientific Workflows: The Key to Convergence?. McCann, M. P.; Hofmann, A. F.; Harmon, T. C.; and Gil, Y. 2012. Ocean Sciences Meeting, Salt Lake City, Utah
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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.; Pierce, M.; Marru, S.; and Wiener, G. 2012. American Geophysical Union Fall Meeting, San Francisco, CA
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Using Semantic Workflows for Genome-Scale Analysis. Gil, Y.; Ratnakar, V.; Deelman, E.; and Mason, C. 2012. International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA
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Reusing Workflow Fragments Across Multiple Data Domains. Sethi, R. J.; Jo, H.; and Gil, Y. In Proceedings of the Seventh Workshop on Workflows in Support of Large-Scale Science (WORKS'12), held in conjunction with SC 2012, Salt Lake City, Utah, 2012.
Reusing Workflow Fragments Across Multiple Data Domains [link]Paper   bibtex   3 downloads
Common Motifs in Scientific Workflows: An Empirical Analysis. Garijo, D.; Alper, P.; Belhajjame, K.; Corcho, O.; Gil, Y.; and Goble, C. In Proceedings of the IEEE Conference on e-Science, Chicago, Illinois, 2012.
Common Motifs in Scientific Workflows: An Empirical Analysis [pdf]Paper   bibtex   2 downloads
  2011 (8)
A Semantic Framework for Automatic Generation of Computational Workflows Using Distributed Data and Component Catalogs. Gil, Y.; Gonzalez-Calero, P. A.; Kim, J.; Moody, J.; and Ratnakar, V. Journal of Experimental and Theoretical Artificial Intelligence, 23(4). 2011.
A Semantic Framework for Automatic Generation of Computational Workflows Using Distributed Data and Component Catalogs [link]Paper   bibtex   12 downloads
A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data. Garijo, D.; and Gil, Y. In Proceedings of the Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS'11), held in conjunction with SC 2011, Seattle, Washington, 2011.
A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data [link]Paper   bibtex   3 downloads
Making Data Analysis Expertise Broadly Accessible through Workflows. Hauder, M.; Gil, Y.; Sethi, R.; Liu, Y.; and Jo, H. In Proceedings of the Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS'11), held in conjunction with SC 2011, Seattle, Washington, 2011.
Making Data Analysis Expertise Broadly Accessible through Workflows [link]Paper   bibtex   11 downloads
A Framework for Efficient Text Analytics through Automatic Configuration and Customization of Scientific Workflows. Hauder, M.; Gil, Y.; and Liu, Y. In Proceedings of the Seventh IEEE International Conference on e-Science, Stockholm, Sweden, 2011.
A Framework for Efficient Text Analytics through Automatic Configuration and Customization of Scientific Workflows [link]Paper   bibtex   7 downloads
Mind Your Metadata: Exploiting Semantics for Configuration, Adaptation, and Provenance in Scientific Workflows. Gil, Y.; Szekely, P.; Villamizar, S.; Harmon, T.; Ratnakar, V.; Gupta, S.; Muslea, M.; Silva, F.; and Knoblock, C. In Proceedings of the Tenth International Semantic Web Conference (ISWC), Bonn, Germany, 2011.
Mind Your Metadata: Exploiting Semantics for Configuration, Adaptation, and Provenance in Scientific Workflows [link]Paper   bibtex
Retrieval of Semantic Workflows with Knowledge Intensive Similarity Metrics. Bergmann, R.; and Gil, Y. In Proceedings of the Nineteenth International Conference on Case Based Reasoning (ICCBR), Greenwich, London, 2011.
Retrieval of Semantic Workflows with Knowledge Intensive Similarity Metrics [link]Paper   bibtex
TellMe: Learning Procedures from Tutorial Instruction. Gil, Y.; Ratnakar, V.; and Fritz, C. In Proceedings of the ACM International Conference on Intelligent User Interfaces, Palo Alto, CA, 2011.
TellMe: Learning Procedures from Tutorial Instruction [link]Paper   bibtex   22 downloads
Wings: Intelligent Workflow-Based Design of Computational Experiments. Gil, Y.; Ratnakar, V.; Kim, J.; Gonzalez-Calero, P. A.; Groth, P.; Moody, J.; and Deelman, E. IEEE Intelligent Systems, 26(1). 2011.
Wings: Intelligent Workflow-Based Design of Computational Experiments [link]Paper   bibtex   18 downloads
  2010 (4)
Assisting Scientists with Complex Data Analysis Tasks through Semantic Workflows. Gil, Y.; Ratnakar, V.; and Fritz, C. In Proceedings of the AAAI Fall Symposium on Proactive Assistant Agents , Arlington, VA, 2010.
Assisting Scientists with Complex Data Analysis Tasks through Semantic Workflows [link]Paper   bibtex
Parameterized Specification, Configuration, and Execution of Data-Intensive Scientific Workflows. Kumar, V.; Kurc, T.; Ratnakar, V.; Kim, J.; Mehta, G.; Vahi, K.; Nelson, Y. L.; Sadayappan, P.; Deelman, E.; Gil, Y.; Hall, M.; and Saltz, J. Cluster Computing Journal, 13(3): 315-333. 2010.
Parameterized Specification, Configuration, and Execution of Data-Intensive Scientific Workflows [link]Link   Parameterized Specification, Configuration, and Execution of Data-Intensive Scientific Workflows [link]Paper   bibtex
Principles for Interactive Acquisition and Validation of Workflows. Kim, J.; Gil, Y.; and Spraragen, M. Journal of Experimental and Theoretical Artificial Intelligence, 22(2): 103-134. 2010.
Principles for Interactive Acquisition and Validation of Workflows [link]Link   Principles for Interactive Acquisition and Validation of Workflows [link]Paper   bibtex   1 download
Reasoning about the Appropriate Use of Private Data through Computational Workflows. Gil, Y.; and Fritz, C. In Proceedings of the AAAI Spring Symposium on Privacy Management, Stanford, CA, 2010.
Reasoning about the Appropriate Use of Private Data through Computational Workflows [link]Paper   bibtex   9 downloads
  2009 (7)
High Performance Computing and Grid Computing for Integrative Biomedical Research. Kurç, T. M.; Hastings, S.; Kumar, V. S.; Langella, S.; Sharma, A.; Pan, T.; Oster, S.; Ervin, D.; Permar, J.; Narayanan, S.; Gil, Y.; Deelman, E.; Hall, M. W.; and Saltz, J. H. Journal of High Performance Computing Applications, 23(3): 252-264. 2009.
High Performance Computing and Grid Computing for Integrative Biomedical Research [link]Link   High Performance Computing and Grid Computing for Integrative Biomedical Research [link]Paper   bibtex
Expressive Reusable Workflow Templates. Gil, Y.; Groth, P.; Ratnakar, V.; and Fritz, C. In Proceedings of the Fifth IEEE International Conference on e-Science (e-Science), Oxford, UK, 2009.
Expressive Reusable Workflow Templates [link]Paper   bibtex   5 downloads
Workflow Matching using Semantic Metadata. Gil, Y.; Kim, J.; Puga, G. F.; Ratnakar, V.; and González-Calero, P. A. In Proceedings of the Fifth International Conference on Knowledge Capture (K-CAP), pages 121-128, Redondo Beach, CA, 2009.
Workflow Matching using Semantic Metadata [link]Link   Workflow Matching using Semantic Metadata [link]Paper   bibtex
Analyzing the Gap between Workflows and their Natural Language Descriptions. Groth, P. T.; and Gil, Y. In Proceedings of the IEEE International Workshop on Scientific Workflows (SWF), pages 299-305, Los Angeles, CA, 2009.
Analyzing the Gap between Workflows and their Natural Language Descriptions [link]Link   Analyzing the Gap between Workflows and their Natural Language Descriptions [link]Paper   bibtex   2 downloads
An Integrated Framework for Performance-Based Optimization of Scientific Workflows. Kumar, V. S.; Sadayappan, P.; Mehta, G.; Vahi, K.; Deelman, E.; Ratnakar, V.; Kim, J.; Gil, Y.; Hall, M. W.; Kurç, T. M.; and Saltz, J. H. In Proceedings of the Eighteenth ACM International Symposium on High Performance Distributed Computing (HPDC), pages 177-186, Garching, Germany, 2009.
An Integrated Framework for Performance-Based Optimization of Scientific Workflows [link]Link   An Integrated Framework for Performance-Based Optimization of Scientific Workflows [link]Paper   bibtex
From Data to Knowledge to Discoveries: Artificial Intelligence and Scientific Workflows. Gil, Y. Scientific Programming, 17(3): 231-246. 2009.
From Data to Knowledge to Discoveries: Artificial Intelligence and Scientific Workflows [link]Link   From Data to Knowledge to Discoveries: Artificial Intelligence and Scientific Workflows [link]Paper   bibtex   2 downloads
A Scientific Workflow Construction Command Line. Groth, P. T.; and Gil, Y. In Proceedings of the ACM International Conference on Intelligent User Interfaces (IUI), pages 445-450, Sanibel Island, FL, 2009.
A Scientific Workflow Construction Command Line [link]Link   A Scientific Workflow Construction Command Line [link]Paper   bibtex
  2008 (3)
Scientific Software as Workflows: From Discovery to Distribution. Woollard, D.; Medvidovic, N.; Gil, Y.; and Mattmann, C. IEEE Software, 25(4): 37-43. 2008.
Scientific Software as Workflows: From Discovery to Distribution [link]Link   Scientific Software as Workflows: From Discovery to Distribution [link]Paper   bibtex
Provenance Trails in the Wings/Pegasus Workflow System. Kim, J.; Deelman, E.; Gil, Y.; Mehta, G.; and Ratnakar, V. Concurrency and Computation: Practice and Experience, Special Issue on the First Provenance Challenge, 20(5). 2008.
Provenance Trails in the Wings/Pegasus Workflow System [link]Paper   bibtex   1 download
Designing and Parameterizing a Workflow for Optimization: A Case Study in Biomedical Imaging. Kumar, V. S.; Hall, M. W.; Kim, J.; Gil, Y.; Kurç, T. M.; Deelman, E.; Ratnakar, V.; and Saltz, J. H. In Proceedings of the Twentysecond IEEE International Symposium on Parallel and Distributed Processing (IPDPS), Miami, FL, 2008.
Designing and Parameterizing a Workflow for Optimization: A Case Study in Biomedical Imaging [link]Link   bibtex
  2007 (6)
Examining the Challenges of Scientific Workflows. Gil, Y.; Deelman, E.; Ellisman, M. H.; Fahringer, T.; Fox, G.; Gannon, D.; Goble, C. A.; Livny, M.; Moreau, L.; and Myers, J. IEEE Computer, 40(12): 24-32. 2007.
Examining the Challenges of Scientific Workflows [link]Link   Examining the Challenges of Scientific Workflows [link]Paper   bibtex
Privacy Enforcement in Data Analysis Workflows. Gil, Y.; Cheung, W. K.; Ratnakar, V.; and Chan, K. In Proceedings of the AAAI Workshop on Privacy Enforcement and Accountability with Semantics (PEAS), held in conjunction with the Sixth International Semantic Web Conference (ISWC) and the Second Asian Semantic Web Conference (ASWC), Busan, Korea, 2007.
Privacy Enforcement in Data Analysis Workflows [link]Paper   bibtex   2 downloads
Wings for Pegasus: Creating Large-Scale Scientific Applications Using Semantic Representations of Computational Workflows. Gil, Y.; Ratnakar, V.; Deelman, E.; Mehta, G.; and Kim, J. In Proceedings of the Twenty-Second National Conference on Artificial Intelligence (AAAI), pages 1767-1774, Vancouver, British Columbia, Canada, 2007.
Wings for Pegasus: Creating Large-Scale Scientific Applications Using Semantic Representations of Computational Workflows [link]Paper   bibtex
Towards Privacy Aware Data Analysis Workflows for e-Science. Cheung, W.; and Gil, Y. In Proceedings of the AAAI Workshop on Semantic e-Science (SeS2007), held in conjunction with the Twenty-Second Conference of the Association for the Advancement of Artificial Intelligence (AAAI), Vancouver, British Columbia, Canada, 2007.
Towards Privacy Aware Data Analysis Workflows for e-Science [link]Paper   bibtex   1 download
On the Black Art of Designing Computational Workflows. Gil, Y.; Gonzalez-Calero, P. A.; and Deelman, E. In Proceedings of the Second Workshop on Workflows in Support of Large-Scale Science (WORKS), held in conjunction with the IEEE International Symposium on High Performance Distributed Computing (HPDC), Monterrey, CA, 2007.
On the Black Art of Designing Computational Workflows [link]Paper   bibtex
Intelligent Optimization of Parallel and Distributed Applications. Bansal, B.; Çatalyürek, Ü. V.; Chame, J.; Chen, C.; Deelman, E.; Gil, Y.; Hall, M. W.; Kumar, V. S.; Kurç, T. M.; Lerman, K.; Nakano, A.; Nelson, Y. L.; Saltz, J. H.; Sharma, A.; and Vashishta, P. In Proceedings of the Twentyfirst International Parallel and Distributed Processing Symposium (IPDPS), Long Beach, CA, 2007.
Intelligent Optimization of Parallel and Distributed Applications [link]Link   bibtex
  2006 (4)
Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges. Deelman, E.; and Gil, Y. In Proceedings of the Workshop on Scientific Workflows and Business Workflow Standards in e-Science of the Second International Conference on e-Science and Grid Technologies (e-Science), Amsterdam, The Netherlands, 2006.
Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges [link]Link   Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges [link]Paper   bibtex
Wings for Pegasus: A Semantic Approach to Creating Very Large Scientific Workflows. Gil, Y.; Kim, J.; Ratnakar, V.; and Deelman, E. In Proceedings of the 2006 Workshop on OWL: Experiences and Directions (OWL-ED), Athens, GA, 2006.
Wings for Pegasus: A Semantic Approach to Creating Very Large Scientific Workflows [pdf]Link   Wings for Pegasus: A Semantic Approach to Creating Very Large Scientific Workflows [link]Paper   bibtex   1 download
Semantic Metadata Generation for Large Scientific Workflows. Kim, J.; Gil, Y.; and Ratnakar, V. In Proceedings of the Fifth International Semantic Web Conference (ISWC), pages 357-370, Athens, GA, 2006.
Semantic Metadata Generation for Large Scientific Workflows [link]Link   Semantic Metadata Generation for Large Scientific Workflows [link]Paper   bibtex
Workflow Composition. Gil, Y. In Workflows for e-Science. Springer Verlag, 2006.
Workflow Composition [link]Paper   bibtex   buy   1 download
  2005 (3)
Simplifying Construction of Complex Workflows for Non-Expert Users of the Southern California Earthquake Center Community Modelling Environment. Maechling, P.; Chalupsky, H.; Dougherty, M.; Deelman, E.; Gil, Y.; Gullapalli, S.; Gupta, V.; Kesselman, C.; Kim, J.; Mehta, G.; Mendenhall, B.; Russ, T.; Singh, G.; Spraragen, M.; Staples, G.; and Vahi, K. ACM SIGMOD Record, Special Issue on Scientific Workflows, 34(3). 2005.
Simplifying Construction of Complex Workflows for Non-Expert Users of the Southern California Earthquake Center Community Modelling Environment [link]Paper   bibtex
Pegasus: A Framework for Mapping Complex Scientific Workflows onto Distributed Systems. Deelman, E.; Singh, G.; Su, M.; Blythe, J.; Gil, Y.; Kesselman, C.; Kim, J.; Mehta, G.; Vahi, K.; Berriman, G. B.; Good, J.; Laity, A.; Jacob, J. C.; and Katz, D. S. Scientific Programming, 13(3). 2005.
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Task scheduling strategies for workflow-based applications in grids. Blythe, J.; Jain, S.; Deelman, E.; Gil, Y.; Vahi, K.; Mandal, A.; and Kennedy, K. In Proceedings of the Fifth International Symposium on Cluster Computing and the Grid (CCGrid), pages 759-767, Cardiff, UK, 2005.
Task scheduling strategies for workflow-based applications in grids [link]Link   bibtex
  2004 (4)
Pegasus: Mapping Scientific Workflows onto the Grid. Deelman, E.; Blythe, J.; Gil, Y.; Kesselman, C.; Mehta, G.; Patil, S.; Su, M.; Vahi, K.; and Livny, M. In Proceedings of the Second European Across Grids Conference (AxGrids), pages 11-20, Nicosia, Cyprus, 2004.
Pegasus: Mapping Scientific Workflows onto the Grid [link]Link   bibtex
Automatically Composed Workflows for Grid Environments. Blythe, J.; Deelman, E.; and Gil, Y. IEEE Intelligent Systems, 19(4): 16-23. 2004.
Automatically Composed Workflows for Grid Environments [link]Link   bibtex
Artificial Intelligence and Grids: Workflow Planning and Beyond. Gil, Y.; Deelman, E.; Blythe, J.; Kesselman, C.; and Tangmunarunkit, H. IEEE Intelligent Systems, 19(1): 26-33. 2004.
Artificial Intelligence and Grids: Workflow Planning and Beyond [link]Link   Artificial Intelligence and Grids: Workflow Planning and Beyond [link]Paper   bibtex
An intelligent assistant for interactive workflow composition. Kim, J.; Spraragen, M.; and Gil, Y. In Proceedings of the ACM International Conference on Intelligent User Interfaces, pages 125-131, Funchal, Madeira, Portugal, 2004.
An intelligent assistant for interactive workflow composition [link]Link   An intelligent assistant for interactive workflow composition [link]Paper   bibtex   1 download
  2003 (4)
Pegasus and the Pulsar Search: From Metadata to Execution on the Grid. Deelman, E.; Blythe, J.; Gil, Y.; Kesselman, C.; Koranda, S.; Lazzarini, A.; Mehta, G.; Papa, M. A.; and Vahi, K. In Applications Grid Workshop at the Fifth International Conference on Parallel Processing and Applied Mathematics (PPAM), pages 821-830, Czestochowa, Poland, 2003.
Pegasus and the Pulsar Search: From Metadata to Execution on the Grid [link]Link   bibtex
Workflow Management in GriPhyN. Deelman, E.; Blythe, J.; Gil, Y.; and Kesselman, C. In Grid Resource Management. Kluwer, 2003.
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Mapping Abstract Workflows onto Grid Environments. Deelman, E.; Blythe, J.; Gil, Y.; Kesselman, C.; Mehta, G.; Vahi, K.; Blackburn, K.; Lazzarini, A.; Arbree, A.; Cavanaugh, R.; and Koranda, S. Journal of Grid Computing, 1(1). 2003.
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Transparent Grid Computing: A Knowledge-Based Approach. Blythe, J.; Deelman, E.; Gil, Y.; and Kesselman, C. In Proceedings of the Fifteenth Conference on Innovative Applications of Artificial Intelligence (IAAI), pages 57-64, Acapulco, Mexico, 2003.
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