Publications

Publications

General Pegasus

2014

McLennan, Michael, Steven Clark, Ewa Deelman, Mats Rynge, Karan Vahi, Frank McKenna, Derrick Kearney, Carol Song. HUBzero and Pegasus: integrating scientific workflows into science gateways. Concurrency and Computation: Practice and Experience, 2014 (Funding Acknowledgements: OCI SI2-SSI program grant #1148515, OCI SDCI program grant #0722019)

Malawski, Maciej, Kamil Figiela, Marian Bubak, Ewa Deelman, Jarek Nabrzyski. Cost Optimization of Execution of Multi-level Deadline-Constrained Scientific Workflows on Clouds. In Parallel Processing and Applied Mathematics, pp. 251-260. Springer Berlin Heidelberg, 2014 (Funding Acknowledgements: OCI SI2-SSI program grant #1148515)

Rafael Ferreira da Silva,  Weiwei Chen, Gideon Juve, Karan Vahi, Ewa Deelman. Community Resources for Enabling Research in Distributed Scientific Workflows. 10th IEEE International Conference on e-Science (eScience 2014), Guarujá, Brazil, 2014 (Funding Acknowledgements: OCI SI2-SSI program grant #1148515, DOE contract for dv/dt ER26110)

Idafen Santana-Perez, Rafael Ferreira da Silva, Mats Rynge, Ewa Deelman, Maria S. Perez-Hernandez, and Oscar Corcho. A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientific Workflows: A Case Study. 1st International Workshop on Reproducibility in Parallel Computing (REPPAR), in conjunction with Euro-Par 2014, Porto, Portugal, 2014 (Funding Acknowledgements: NSF FutureGrid 0910812)

Rafael Ferreira da Silva, Thomas Fahringer, Juan J. Durillo, Ewa Deelman.  A Unified Approach for Modeling and Optimization of Energy, Makespan and Reliability for Scientific Workflows on Large-Scale Computing Infrastructures. Workshop on Modeling & Simulation of Systems and Applications, (MODSIM), Seattle, USA, 2014 (Funding Acknowledgements: DOE contract for dv/dt ER26110).

Tristan Glatard, Lindsay B Lewis, Rafael Ferreira da Silva, Marc-Etienne Rousseau, Claude Lepage, Pierre Rioux, Najmeh Mahani, Ewa Deelman, Alan C Evans. Extending provenance information in CBRAIN to address reproducibility issues across computing platforms. NeuroInformatics 2014, Leiden, The Netherlands, 2014.

Idafen Santana-Perez, Rafael Ferreira da Silva, Mats Rynge, Ewa Deelman, Maria S. Perez-Hernandez, and Oscar Corcho. Leveraging Semantics to Improve Reproducibility in Scientific Workflows. The reproducibility at XSEDE workshop, Atlanta, USA, 2014 (Funding Acknowledgements: NSF FutureGrid 0910812)

2013

Anirban Mandal, Paul Ruth, Ilya Baldin, Yufeng Xin, Claris Castillo, Mats Rynge, Ewa Deelman. Evaluating I/O Aware Network Management for Scientific Workflows on Networked Clouds. The 3rd International Workshop on Network-aware Data Management, in conjunction with SC'13, Denver, CO. (Funding Acknowledgements:  NSF CC-NIE ADAMANT pro ject (NSF ACI 1245926), DoE DROPS project (ASCR DE-SC0005286), DoE SciDAC SUPER (DE-FG02- 11ER26050/DE-SC0006925) pro ject, NSF SDCI Missing Link pro ject (NSF ACI 1032573), and the NSF GENI pro ject (GENI Pro ject Office Award #1872)
 
Weiwei Chen, Rafael Ferreira da Silva, Ewa Deelman, and Rizos Sakellariou. Balanced Task Clustering in Scientific Workflows. 9th IEEE International Conference on e-Science (eScience 2013), Beijing, China, Oct 24, 2013 (Funding Acknowledgements: NFS IIS-0905032 and NSF FutureGrid 0910812)
 
Mats Rynge, Gideon Juve , Jamie Kinney , John Good, Bruce Berriman, Ann Merrihew, and Ewa Deelman. Producing an Infrared Multiwavelength Galactic Plane Atlas using Montage, Pegasus and Amazon Web Services.  23rd Annual Astronomical Data Analysis Software and Systems (ADASS) Conference. (Funding Acknowledgments: OCI SI2-SSI program grant #1148515).

Rafael Ferreira Da Silva, Gideon Juve, Ewa Deelman, Tristan Glatard, Frederic Desprez, Douglas Thain, Benjamín Tovar and Miron Livny. Toward Fine-Grained Online Task Characteristics Estimation in Scientific Workflows8th Workshop On Workflows in Support of Large-Scale Science, 2013(Funding Acknowledgements: DOE contract for dv/dt ER26110, EC FP7 Programme under grant agreement 312579 ER-flow)

Sepideh Azarnoosh, Mats Rynge, Gideon Juve, Ewa Deelman Michal Nieć, Maciej Malawski, Rafael Ferreira da Silva. Introducing PRECIP: An API for Managing Repeatable Experiments in the CloudWorkshop on Cloud Computing for Research Collaborations (CRC), 2013. (Funding Acknowledgements: National Science Foundation under Grant No. 0910812 and AWS Educational Grant)

Weiwei Chen, Ewa Deelman, and Rizos Sakellariou. Imbalance Optimization in Scientific Workflows. International Conference on Supercomputing (ICS 2013), 2013 (Funding Acknowledgements: NFS IIS-0905032 and NSF FutureGrid 0910812)

Karan Vahi, Mats Rynge, Gideon Juve, Rajiv Mayani, and Ewa Deelman.  Rethinking Data Management for Big Data Scientific Workflows.  Workshop on Big Data and Science: Infrastructure and Services, 2013 (Funding Acknowledgments: OCI SDCI program grant #0722019 and OCI SI2-SSI program grant #1148515).

Ilia Pietri, Maciej Malawski, Gideon Juve, Ewa Deelman, Jarek Nabrzyski, Rizos Sakellariou.  Energy-Constrained Provisioning for Scientific Workflow Ensembles IEEE International Conference on Cloud and Green Computing (CGC’13), 2013.

Gideon Juve, Mats Rynge, Ewa Deelman, Jens-S. Vockler, G. Bruce Berriman.  Comparing FutureGrid, Amazon EC2, and Open Science Grid for Scientific Workflows Computing in Science and Engineering, 15:4, pp. 20-29, 2013. (Funding: NSF OCI-0943725 and OCI-0910812, Amazon Web Services Educational Grant).

Ewa Deelman, Gideon Juve, Maciej Malawski, Jarek Nabrzyski.  Hosted Science: Managing Computational Workloads in the Cloud Parallel Processing Letters, 23:2, June 2013. (Funding: NSF OCI-0943725 and OCI-1148515)

Michael McLennan, Steve Clark, Frank McKenna, Ewa Deelman, Mats Rynge, Karan Vahi, Derrick Kearney, Carol Song: Bringing Scientific Workflow to the Masses via Pegasus and HUBzero. Proceedings of the 5th International Workshop on Science Gateways, Zurich, Switzerland, 3-5 June, 2013. (Funding Acknowledgements: NSF grants CBET-0941302, CMMI-0927178, OCI-1148515, and OCI-0943705)

Karan Vahi, Ian Harvey, Taghrid Samak, Daniel Gunter, Kieran Evans, David Rogers, Ian Taylor, Monte Goode, Fabio Silva, Eddie Al-Shakarchi, Gaurang Mehta, Ewa Deelman, Andrew Jones.  A Case Study into Using Common Real-Time Workflow Monitoring Infrastructure for Scientific Workflows.  Journal of Grid Computing: Volume 11, Issue 3 (2013), Page 381-406. (Funding Acknowledgements:  NSF grant OCI-0943705)  

G. B. Berriman, G. Juve, J-S. Vöckler, E. Deelman, M. Rynge.  The Application of Cloud Computing to Scientific Workflows: A Study of Cost and Performance.  Proceedings of the Royal Society A, 28 vol. 371, no 1983, January 2013 (Funding Acknowledgements: NSF OCI-0910812, NSF OCI-0943725, NASA NCC5-626, and Amazon Educational Grant)  

Gideon Juve, Ann Chervenak, Ewa Deelman, Shishir Bharathi, Gaurang Mehta, Karan Vahi.  Characterizing and Profiling Scientific Workflows.  Future Generation Computer Systems, vol. 29, no. 3, pp. 682-692, March 2013.  

2012

Karan Vahi, Ian Harvey, Taghrid Samak, Dan Gunter, Kieran Evans, David Rogers, Ian Taylor, Monte Goode, Fabio Silva, Eddie Al-Shakarchi, Gaurang Mehta, Andrew Jones, Ewa Deelman.  A General Approach to Real-time Workflow Monitoring.  The 7th Workshop on Workflows in Support of Large-Scale Science (WORKS'12), Salt Lake City, November 10-16, 2012 (Funding Acknowledgement: NSF OCI-0943705)  

Ann L. Chervenak, David E. Smith, Weiwei Chen, Ewa Deelman.  Integrating Policy with Scientific Workflow Management for Data-Intensive Applications.  The 7th Workshop on Workflows in Support of Large-Scale Science (WORKS'12), Salt Lake City, November 10-16, 2012 (Funding Acknowledgement: NFS IIS-0905032 and FutureGrid 0910812) 

Rohit Agarwal, Gideon Juve, Ewa Deelman.  Peer-to-Peer Data Sharing for Scientific Workflows on Amazon EC2.  7th Workshop on Workflows in Support of Large-Scale Science (WORKS'12), 2012. (Funding Acknowledgement: NSF OCI-0943725, Viterbi-India Program)  

G. Bruce Berriman, Carolyn Brinkworth, Dawn Gelino, Dennis K. Wittman, Ewa Deelman, Gideon Juve, Mats Rynge, Jamie Kinney.  A Tale Of 160 Scientists, Three Applications, A Workshop and A Cloud.  Astronomical Data Analysis Software and Systems XXII, 2012.  

Weiwei Chen, Ewa Deelman.  WorkflowSim: A Toolkit for Simulating Scientific Workflows in Distributed Environments.  The 8th IEEE International Conference on eScience 2012 (eScience 2012), Chicago, Oct 8-12, 2012. (Funding Acknowledgement: NFS IIS-0905032)  

Taghrid Samak, Dan Gunter, Monte Goode, Ewa Deelman, Gideon Juve, Fabio Silva.  Failure Analysis of Distributed Scientific Workflows Executing in the Cloud.  8th International Conference on Network and Service Management (CNSM 2012), 2012. (Funding Acknowledgements: DOE DE-AC02-05CH11231 and NSF OCI-0943705)  

Maciej Malawski, Gideon Juve, Ewa Deelman, Jarek Nabrzyski.  Cost- and Deadline-Constrained Provisioning for Scientific Workflow Ensembles in IaaS Clouds.  24th IEEE/ACM International Conference on Supercomputing (SC12), 2012. (Funding Acknowledgements: NSF OCI-0943725)  

Gideon Juve, Ewa Deelman, Bruce Berriman, Benjamin P. Berman, Phil Maechling.  An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2.  Journal of Grid Computing, vol. 10, no. 1, pp. 5-21, 2012. (Funding Acknowledgements: NSF CCF-0725332, NSF OCI-0722019, and NASA NCC5-626)  

Ewa Deelman, Gideon Juve, G. Bruce Berriman.  Using Clouds for Science, Is it Just Kicking the Can Down The Road?  2nd International Conference on Cloud Computing and Services Science (CLOSER 2012), 2012. (Funding Acknowledgements: NSF OCI-0943725)  

Mats Rynge, Gideon Juve, Karan Vahi, Scott Callaghan, Gaurang Mehta, Philip J. Maechling, Ewa Deelman.  Enabling Large-scale Scientific Workflows on Petascale Resources Using MPI Master/Worker.  XSEDE'12, July 2012.  (Funding acknowledgements:  NSF OCI-0722019, NSF OCI-0943725, NSF EAR-0529922, USGS 07HQAG0008, NSF OCI-1053575)  

Weiwei Chen, Ewa Deelman.  Fault Tolerant Clustering in Scientific Workflows.  IEEE 6th International Workshop on Scientific Workflows (SWF 2012) in conjunction with IEEE 8th World Congress on Services (SERVICES 2012), Honolulu, Hawaii, June 24, 2012. (Funding Acknowledgement: NFS IIS-0905032)  

Weiwei Chen, Ewa Deelman.  Integration of Workflow Partitioning and Resource Provisioning.  The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), Doctoral Symposium, Ottawa, Canada, May 14, 2012. (Funding Acknowledgement: NFS IIS-0905032)  

2011

Mats Rynge, Gideon Juve, Gaurang Mehta, Ewa Deelman, Krista Larson, Burt Holzman, Igor Sfiligoi, Frank Würthwein, G. Bruce Berriman, Scott Callaghan.  Experiences Using GlideinWMS and the Corral Frontend Across Cyberinfrastructures.  Proceedings of the 7th IEEE International Conference on e-Science (e-Science 2011), December 2011. (Funding Acknowledgements: Open Science Grid, NSF OCI-0943725, and TeraGrid TG-CCR1000018)  

Gideon Juve, Ewa Deelman.  Automating Application Deployment in Infrastructure Clouds.  3rd IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2011), 2011. (Funding Acknowlegements: DOE, NSF OCI-0943725, and NSF OCI-091812)  

Ashish Nagavaram, Gagan Agrawal, Michael Freitas, Gaurang Mehta, Rajiv Mayani, Ewa Deelman.  A Cloud‐based Dynamic Workflow for Mass Spectrometry Data Analysis.  Proceedings of the 7th IEEE International Conference on e-Science (e-Science 2011), December 2011.  

Weiwei Chen, Ewa Deelman.  Workflow Overhead Analysis and Optimizations.  6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11), Seattle, Washington, November 14th, 2011.  (Funding Acknowledgements: NFS IIS-0905032)

Taghrid Samak, Dan Gunter, Monte Goode, Ewa Deelman, Gaurang Mehta, Fabio Silva, Karan Vahi.  Failure Prediction and Localization in Large Scientific Workflows.  6th Workshop on Workflows in Support of Large-Scale Science (WORKS 11), Seattle, Washington, November 14th, 2011.  

Dan Gunter, Ewa Deelman, Taghrid Samak, Christopher Brooks, Monte Goode, Gideon Juve, Gaurang Mehta, Priscilla Moraes, Fabio Silva, Martin Swany, Karan Vahi.  Online Workflow Management and Performance Analysis with Stampede.  7th International Conference on Network and Service Management (CNSM-2011), Paris, France, October 2011.  

Weiwei Chen, Ewa Deelman.  Partitioning and Scheduling Workflows across Multiple Sites with Storage Constraints.  9th International Conference on Parallel Processing and Applied Mathmatics, Torun, Poland, September 2011.  (Funding Acknowledgements: NFS IIS-0905032)

Taghrid Samak, Dan Gunter, Ewa Deelman, Gideon Juve, Gaurang Mehta, Fabio Silva, Karan Vahi.  Online Fault and Anomaly Detection for Large-Scale Scientific Workflows.  13th IEEE International Conference on High Performance Computing and Communications (HPCC-2011), Banff, Alberta, Canada, September 2011. (Funding Acknowledgements: DOE DE-AC02-05CH11231, and NSF OCI-0943705)  

Scott Callaghan, Philip Maechling, Patrick Small, Kevin Milner, Gideon Juve, Thomas H. Jordan, Ewa Deelman, Gaurang Mehta, Karan Vahi, Dan Gunter, Keith Beattie.  Metrics for Heterogeneous Scientific Workflows: A Case Study of an Earthquake Science Application.  International Journal of High Performance Computing Applications, 25:3, pp. 274-285, August 2011. (Funding Acknowledgements: TeraGrid TG-MCA03S012, NSF OCI-0722019, NSF OCI-0749313, NSF EAR-0106924 and USGS 02HQAG0008)  

Gaurang Mehta, Ewa Deelman, James A Knowles, Ting Chen, Ying Wang, Jens Vöckler, Steven Buyske, Tara Matise.  Enabling Data and Compute Intensive Workflows in Bioinformatics.  2nd International Workshop onHigh Performance Bioinformatics and Biomedicine (HiBB 2011) in conjunction with Euro-Par Conference 2011, Bordeaux France, Aug 29-30, 2011.  

Ying Wang, Gaurang Mehta, Rajiv Mayani, Jingxi Lu, Tade Souaiaia, Yangho Chen, Andrew Clark, Hee Jae Yoon, Lin Wan, Oleg V. Evgrafov, James A. Knowles, Ewa Deelman, and Ting Chen.  RseqFlow: Workflows for RNA-Seq Data Analysis.  Bioinformatics (2011) first published online July 27, 2011 doi:10.1093/bioinformatics/btr441.  

Eun-Kyu Byun, Yang-Suk Kee, Jin-Soo Kim, Ewa Deelman, Seungryoul Maeng.  BTS: Resource Capacity Estimate for Time-targeted Science Workflows, Journal of Parallel and Distributed Computing.  Volume 71, Issue 6, Special Issue on Cloud Computing, June 2011, Pages 848-862, ISSN 0743-7315, DOI: 10.1016/j.jpdc.2011.01.008.  

G. Bruce Berriman, John Good, Ewa Deelman and Anastasia Alexov.  Ten years of software sustainability at the Infrared Processing and Analysis Center.  Phil. Trans. R. Soc. A 2011 369, 3384-3397, doi: 10.1098/rsta.2011.0136.  

Gideon Juve and Ewa Deelman.  Wrangler: Virtual Cluster Provisioning for the Cloud.  Short paper, Proceedings of the 20th International Symposium on High Performance Distributed Computing (HPDC'11), 2011. (Funding Acknowledgements: NSF OCI-0943725)  

Jens-S. Vöckler, Gideon Juve, Ewa Deelman, Mats Rynge, G. Bruce Berriman.  Experiences Using Cloud Computing for A Scientific Workflow Application.  Proceedings of 2nd Workshop on Scientific Cloud Computing (ScienceCloud 2011), 2011. (Funding Acknowledgements: NSF OCI-0910812)  

2010

Mirko Sonntag Dimka Karastoyanova and Ewa Deelman.  Bridging The Gap Between Business And Scientific Workflows.  e-Science 2010, Brisbane, Australia.  

G. Bruce Berriman, Gideon Juve, Ewa Deelman, Moira Regelson, Peter Plavchan.  The Application of Cloud Computing to Astronomy: A Study of Cost and Performance.  In Workshop on e-Science challenges in Astronomy and Astrophysics in conjunction with the 6th IEEE International Conference on e-Science (e-Science 2010), December 2010. (Funding Acknowledgements: NSF OCI-0438712, and NSF CCF-0725332)  

Rizos Sakellariou, Henan Zhao, Ewa Deelman.  Mapping Workflows on Grid Resources: Experiments with the Montage Workflow.  In Grids, P2P and Services Computing, Springer, 2010, pp. 119-132.  

Mirko Sonntag, Dimka Karastoyanova and Ewa Deelman.  BPEL4Pegasus: Combining Business and Scientific Workflows.  International Conference on Service-Oriented Computing (ICSOC), San Francisco, California, December 2010.  

Raphael Bolze and Ewa Deelman.  Exploiting the Cloud of Computing Environments: An Application¹s Perspective.  Cloud Computing and Software Services: Theory and Techniques, Editors Syed A. Ahson and Mohammad Ilyas, CRC Press, July 2010.  

Robert Graves, Thomas Jordan, Scott Callaghan, Ewa Deelman, Edward Field, Gideon Juve, Carl Kesselman, Philip Maechling, Gaurang Mehta, Kevin Milner, David Okaya, Patrick Small, Karan Vahi.  CyberShake: A Physics-Based Seismic Hazard Model for Southern California.  Pure and Applied Geophysics, May 2010. (Funding Acknowledgements: NSF OCI-0438712, NSF CCF-0725332)  

Gideon Juve, Ewa Deelman, Karan Vahi, Gaurang Mehta.  Experiences with Resource Provisioning for Scientific Workflows Using Corral.  Scientific Programming, 18:2, pp. 77-92, April 2010. (Funding Acknowledgements: NSF OCI-0943725 and NSF OCI-0749313)  

G. Bruce Berriman, Ewa Deelman, Paul Groth, and Gideon Juve.  The Application of Cloud Computing to the Creation of Image Mosaics and Management of Their Provenance.  SPIE Conference 7740: Software and Cyberinfrastructure for Astronomy, 2010.  

Gideon Juve, Ewa Deelman, Karan Vahi, Gaurang Mehta, Bruce Berriman, Benjamin P. Berman, Phil Maechling.  Data Sharing Options for Scientific Workflows on Amazon EC2.  22nd IEEE/ACM Conference on Supercomputing (SC10), New Orleans, Louisiana, November 2010. (Funding Acknowledgments: NSF CCF-0725332, NSF OCI-0722019, and NASA NCC5-626)  

Scott Callaghan, Ewa Deelman, Dan Gunter, Gideon Juve, Philip Maechling, Christopher Brooks, Karan Vahi, Kevin Milner, Robert Graves, Edward Field, David Okaya, Thomas Jordan.  Scaling up Workflow-based Applications.  Journal of Computer and System Sciences, 76:6, pp. 428-446,September 2010. (Funding Acknowledgements: TeraGrid TG-MCA03S012, NSF OCI-0722019, and NSF OCI-0749313)  

Vijay S. Kumar, Tahsin Kurc, Varun Ratnakar, Jihie Kim, Gaurang Mehta, Karan Vahi, Yoonju Lee Nelson, P. Sadayappan, Ewa Deelman, Yolanda Gil, Mary Hall and Joel Saltz.  Parameterized Specification, Configuration and Execution of Data-intensive Scientific Workflows.   2010 Cluster Computing Journal, 13(3):315-333.  

Gideon Juve, Ewa Deelman.  Scientific Workflows and Clouds.  ACM Crossroads, 16:3, pp. 14-18, Spring 2010.  

2009

Kevin Lee, Norman W. Paton, Rizos Sakellariou, Ewa Deelman, Alvaro A. A. Fernandes, Gaurang Mehta.  Adaptive Workflow Processing and Execution in Pegasus. In Concurrency and Computation: Practice and Experience.  Volume 21, issue 16, 2009, pages 1965-1981.  

Ewa Deelman.  Grids and Clouds: Making Workflow Applications Work in Heterogeneous Distributed Environments.  International Journal of High Performance Computing Applications. 2009.  

Gideon Juve, Ewa Deelman, Karan Vahi, Gaurang Mehta, Bruce Berriman, Benjamin P. Berman and Phil Maechling.  Scientific Workflow Applications on Amazon EC2.  Workshop on Cloud-based Services and Applications in conjunction with 5th IEEE International Conference on e-Science (e-Science 2009), Oxford UK, December 9-11, 2009.  

Paul Groth, Ewa Deelman, Gideon Juve, Gaurang Mehta, Bruce Berriman.  Pipeline-Centric Provenance Model.  4th Workshop on Workflows in Support of Large-Scale Science (WORKS 09) in conjunction with 21st IEEE/ACM conference on Supercomputing (SC 09), November 2009.  

Vijay S. Kumar, P. Sadayappan, Gaurang Mehta, Karan Vahi, Ewa Deelman, Varun Ratnakar, Jihie Kim, Yolanda Gil, Mary W. Hall, Tahsin M. Kurç, Joel H. Saltz.  An Integrated Framework for Performance-based Optimization of Scientific Workflows.  HPDC 2009: 177-186.  

Rizos Sakellariou and Henan Zhao and Ewa Deelman.  Mapping Workflows on Grid Resources: Experiments with the Montage Workflow CoreGrid 2009.  

2008

Gideon Juve, Ewa Deelman.  Resource Provisioning Options for Large-Scale Scientific Workflows.  Third International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008), 10 December 2008 in Indianapolis, Indiana, USA.  

Scott Callaghan, Philip Maechling, Ewa Deelman, Karan Vahi, Gaurang Mehta, Gideon Juve, Kevin Milner, Robert Graves, Edward Field, David Okaya, Dan Gunter, Keith Beattie, Thomas Jordan.  Reducing Time-to-Solution Using Distributed High-Throughput Mega-Workflows - Experiences from SCEC CyberShake.  Fourth IEEE International Conference on e-Science (e-Science 2008), 10-12 December 2008 in Indianapolis, Indiana, USA.  

Christina Hoffa, Gaurang Mehta, Timothy Freeman, Ewa Deelman, Kate Keahey, Bruce Berriman, John Good.  On the Use of Cloud Computing for Scientific Workflows.  3rd International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBES) in conjunction with Fourth IEEE International Conference on e-Science (e-Science 2008), 10 December 2008 in Indianapolis, Indiana, USA.  

Shishir Bharathi, Ann Chervenak, Ewa Deelman, Gaurang Mehta, Mei-Hui Su, Karan Vahi.  Characterization of Scientific Workflows.  3rd Workshop on Workflows in Support of Large-Scale Science (WORKS08), Austin, TX, November 2008.  

Ewa Deelman, Dennis Gannon, Matthew Shields, Ian Taylor.  Workflows and e-Science: An Overview of Workflow System Features and Capabilities.  Future Generation Computer Systems, July 10th 2008.  

Ewa Deelman, Ann Chervenak.  Data Management Challenges of Data-Intensive Scientific Workflows.  3rd International Workshop on Workflow Systems in e-Science (WSES 08), in conjunction with CCGrid 2008 Conference, Lyon, France, May 20, 2008.  

Ewa Deelman, Gurmeet Singh, Miron Livny, Bruce Berriman, John Good.  The Cost of Doing Science on the Cloud: The Montage Example.  Proceeding of Super Computing 2008, Austin, Texas.  

K.Lee, N. W. Paton, R. Sakellariou, E. Deelman, A. A. A. Fernandes, G. Mehta.  Adaptive Workflow Processing and Execution in Pegasus.  3rd International Workshop on Workflow Management and Applications in Grid Environments (WaGe08), in Proceedings of the Third International Conference on Grid and Pervasive Computing Symposia/Workshops, Pages 99-106, ISBN 978-0-7695-3177-9, May 25-28 2008, Kunming, China.  

Miles, S.; Groth, P.; Deelman, E.; Vahi, K.; Mehta, G.; Moreau, L.  Provenance: The Bridge Between Experiments and Data.  Computing in Science & Engineering Volume:10 Issue:3 May-June 2008 Page(s):38-46.  

Gurmeet Singh, Mei-Hui Su, Karan Vahi, Ewa Deelman, Bruce Berriman, John Good, Daniel S. Katz, and Gaurang Mehta.  Workflow Task Clustering for Best Effort Systems with Pegasus.  Mardi Gras Conference, Baton Rouge, LA, January 2008.  

2007

Gil, Y.; Deelman, E.; Ellisman, M.; Fahringer, T.; Fox, G.; Gannon, D.; Goble, C.; Livny, M.; Moreau, L.; Myers, J.  Examining the Challenges of Scientific Workflows.  Computer , Vol.40, no.12, pp.24-32, Dec. 2007.  

Simon Miles, Ewa Deelman, Paul Groth, Karan Vahi, Gaurang Mehta, Luc Moreau.  Connecting Scientific Data to Scientific Experiments with Provenance.  Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007) 10-13 December 2007 in Bangalore, India.  

Jihie Kim, Ewa Deelman, Yolanda Gil, Gaurang Mehta, Varun Ratnakar.  Provenance Trails in the Wings/Pegasus Workflow System.  Concurrency and Computation: Practice and Experience, Special Issue on the First Provenance Challenge, 2007.  

Ann Chervenak, Ewa Deelman, Miron Livny, Mei-Hui Su, Rob Schuler, Shishir Bharathi, Gaurang Mehta, Karan Vahi.  Data Placement for Scientific Applications in Distributed Environments.  Proceedings of Grid Conference 2007, Austin, Texas, September 2007.  

Gurmeet Singh, Karan Vahi, Arun Ramakrishnan, Gaurang Mehta, Ewa Deelman, Henan Zhao, Rizos Sakellariou,Kent Blackburn, Duncan Brown, Stephen Fairhurst, David Meyers, G. Bruce Berriman.  Optimizing Workflow Data Footprint.  Special issue of the Scientific Programming Journal dedicated to Dynamic Computational Workflows: Discovery, Optimisation and Scheduling, 2007.  

Yolanda Gil, Varun Ratnakar, Ewa Deelman, Gaurang Mehta, and Jihie Kim.  Wings for Pegasus: Creating Large-Scale Scientific Applications Using Semantic Representations of Computational Workflows.  Proceedings of the 19th Annual Conference on Innovative Applications of Artificial Intelligence (IAAI), Vancouver, British Columbia, Canada, July 22-26, 2007.  

Nandita Mandal, Ewa Deelman, Gaurang Mehta, Mei-Hui Su, and Karan Vahi.  Integrating Existing Scientific Workflow Systems: The Kepler/Pegasus Example.  Proceedings of the Second Workshop on Workflows in Support of Large-Scale Science (WORKS'07), in conjunction with the IEEE International Symposium on High Performance Distributed Computing Monterrey, CA, June 2007.  

Arun Ramakrishnan, Gurmeet Singh, Henan Zhao, Ewa Deelman, Rizos Sakellariou, Karan Vahi, Kent Blackburn , David Meyers and Michael Samidi.  Scheduling Data-Intensive Workflows onto Storage-Constrained Distributed Resources Seventh IEEE International Symposium on Cluster Computing and the Grid - CCGrid 2007.  

2006

Jens Voeckler, Gaurang Mehta, Yong Zhao, Ewa Deelman, Mike Wilde.  Kickstarting Remote Applications.  Presented at GCE06 Second International Workshop on Grid Computing Environments Tampa Florida.  

Ewa Deelman, Yolanda Gil.  Managing Large-Scale Scientific Workflows in Distributed Environments: Experiences and Challenges.  Workflows in e-Science, e-Science 2006, Amsterdam, December 4-6, 2006.  

Gurmeet Singh, Carl Kesselman, Ewa Deelman.  Application-level Resource Provisioning on the Grid.  e-Science 2006, Amsterdam, December 4-6, 2006.  

A. Lathers, M.-H. Su, A. Kulungowski, A. W. Lin, G. Mehta, S. T. Peltier, Ewa Deelman, and M. H. Ellisman.  Enabling Parallel Scientific Applications with Workflow Tools.  Proceedings of Challenges of Large Applications in Distributed Environments (CLADE), Paris, 2006.

2005

Ewa Deelman, Gurmeet Singh, Mei-Hui Su, James Blythe, Yolanda Gil, Carl Kesselman, Gaurang Mehta, Karan Vahi, G. Bruce Berriman, John Good, Anastasia Laity, Joseph C. Jacob, Daniel S. Katz.  Pegasus: a Framework for Mapping Complex Scientific Workflows onto Distributed Systems.  Scientific Programming Journal, Vol 13(3), 2005, Pages 219-237.

Philip Maechling, Hans Chalupsky, Maureen Dougherty, Ewa Deelman, Yolanda Gil, Sridhar Gullapalli, Vipin Gupta, Carl Kesselman, Jihie Kim, Gaurang Mehta, Brian Mendenhall, Thomas A. Russ, Gurmeet Singh, Marc Spraragen, Garrick Staples, Karan Vahi.  Simplifying construction of complex workflows for non-expert users of the Southern California Earthquake Center Community Modeling Environment.  SIGMOD Record 34(3): 24-30 (2005).

J Blythe, S Jain, E Deelman, Y Gil, K Vahi, A Mandal,K Kennedy.  Task Scheduling Strategies for Workflow-based Applications in Grids.  CCGrid 2005, Cardiff, UK.

Gurmeet Singh,Carl Kesselman, Ewa Deelman.  Optimizing Grid-Based Workflow Execution.  Journal of Grid Computing, Volume 3(3-4), December 2005, Pages 201-219.

G Singh, E Deelman, G Mehta, K Vahi, Mei Su, B. Berriman, J Good, J Jacob, D Katz, A Lazzarini, K Blackburn, S Koranda.  The Pegasus Portal: Web Based Grid Computing.  The 20th Annual ACM Symposium on Applied Computing, Santa Fe, New Mexico, March 13 -17, 2005.

2004

Ewa Deelman, James Blythe, Yolanda Gil, Carl Kesselman, Gaurang Mehta, Sonal Patil, Mei-Hui Su, Karan Vahi, Miron Livny.  Pegasus : Mapping Scientific Workflows onto the Grid.  Across Grids Conference 2004, Nicosia, Cyprus.  

2003

Ewa Deelman, James Blythe, Yolanda Gil, Carl Kesselman, Scott Koranda, Albert Lazzarini, Gaurang Mehta, Maria Alessandra Papa, Karan Vahi.  Pegasus and the Pulsar Search: From Metadata to Execution on the Grid.  Applications Grid Workshop, PPAM 2003, Czestochowa, Poland 2003.

Ewa Deelman, James Blythe, Yolanda Gil, and Carl Kesselman.  Workflow Management in GriPhyN.  In Grid Resource Management, J. Nabrzyski, J. Schopf, and J. Weglarz editors, Kluwer 2003.

Ewa Deelman, James Blythe, Yolanda Gil, Carl Kesselman, Gaurang Mehta, Karan Vahi, Kent Blackburn, Albert Lazzarini, Adam Arbree, Richard Cavanaugh, and Scott Koranda.  Mapping Abstract Complex Workflows onto Grid Environments.  Journal of Grid Computing, Vol.1, no. 1, 2003, pp. 25-39.

Using AI Techniques for Workflow Mapping

Yolanda Gil, Varun Ratnakar, Ewa Deelman et al.  Wings: Intelligent Workflow-Based Design of Computational Experiments.  Intelligent Systems, IEEE. January 2010.

Yolanda Gil, Ewa Deelman, Jim Blythe, Carl Kesselman, and Hongsuda Tangmurarunkit.  Artificial Intelligence and Grids: Workflow Planning and Beyond.  IEEE Intelligent Systems, January 2004.

Jim Blythe, Ewa Deelman, Yolanda Gil, Carl Kesselman.  Transparent Grid Computing: a Knowledge-Based Approach.  IAAI 2003.

Jim Blythe, Ewa Deelman, Yolanda Gil, Carl Kesselman, Amit Agarwal, Gaurang Mehta, Karan Vahi.  The Role of Planning in Grid Computing.  ICAPS 2003.

Jim Blythe, Ewa Deelman, Yolanda Gil.  Planning for workflow construction and maintenance on the Grid.  ICAPS 2003 Workshop on Planning for Web Services.

Ewa Deelman, James Blythe, Yolanda Gil, Carl Kesselman.  Pegasus: Planning for Execution in Grids.  GriPhyN technical report 2002-20.

Ewa Deelman James Blythe Yolanda Gil Carl Kesselman Gaurang Mehta Karan Vahi, Scott Koranda, Albert Lazzarini, Maria Alessandra Papa.  From Metadata to Execution on the Grid Pegasus and the Pulsar Search.  GriPhyN technical report 2003-15.

Papers on Applications Using Pegasus

Ewa Deelman, Scott Callaghan, Edward Field, Hunter Francoeur, Robert Graves, Nitin Gupta, Vipin Gupta, Thomas H. Jordan, Carl Kesselman, Philip Maechling, John Mehringer, Gaurang Mehta, David Okaya, Karan Vahi, Li Zhao.  Managing Large-Scale Workflow Execution from Resource Provisioning to Provenance tracking: The CyberShake Example.  e-Science 2006, Amsterdam, December 4-6, 2006. BEST PAPER AWARD

Veronika Nefedova, Robert Jacob, Ian Foster, Zhengyu Liu, Yun Liu, Ewa Deelman, Gaurang Mehta, Mei-Hui Su, Karan Vahi.  Automating Climate Science: Large Ensemble Simulations on the TeraGrid with the GriPhyN Virtual Data System.  e-Science 2006, Amsterdam, December 4-6, 2006.

Daniel S. Katz, Joseph C. Jacob, G. Bruce Berriman, John Good, Anastasia C. Laity, Ewa Deelman, Carl Kesselman, Gurmeet Singh, Mei-Hui Su, Thomas A. Prince.  Comparison of Two Methods for Building Astronomical Image Mosaics on a Grid.  Parallel Processing, 2005. ICPP 2005 Workshops. International Conference Workshops on , pp. 85- 94, 14-17 June 2005 Paper on Applications using Pegasus.

Ewa Deelman, Raymond Plante, Carl Kesselman, Gurmeet Singh, Mei-Hui Su, Gretchen Greene, Robert Hanisch, Niall Gaffney, Antonio Volpicelli, James Annis, Vijay Sekhri, Tamas Budavari, Maria Nieto-Santisteban, William O’Mullane, David Bohlender, Tom McGlynn, Arnold Rots, Olga Pevunova.  Grid-Based Galaxy Morphology Analysis for the National Virtual Observatory.  Proceedings of SC 2003.

G. B. Berriman , J. C. Good, A. C. Laity, A. Bergou, J. Jacob, D. S. Katz, E. Deelman, C. Kesselman, G. Singh, M.-H. Su, R. Williams.  Montage A Grid Enabled Image Mosaic Service for the National Virtual Observatory.  ADASS XIII, ASP Conference Series Vol XXX, F Ochsenbein M Allen and D Egret eds, 2003.

Gurmeet Singh, Ewa Deelman.  Montage on the Grid.  NVO Technical Report, April 3, 2003.  For more information on Montage, please visit http://montage.ipac.caltech.edu/

R. Williams, B. Berriman, E. Deelman, J. Good, J. Jacob, C. Kesselman, C. Lonsdale, S. Oliver, T. Prince.  Multi-Wavelength Image Space: Another Grid-Enabled Science.  Journal of Concurrency and Computation: Practice and Experience, Wiley, March 2003.

E. Deelman, C. Kesselman, G. Mehta, L. Meshkat, L. Pearlman, K. Blackburn, P. Ehrens, A. Lazzarini, R. Williams, S. Koranda. GriPhyN and LIGO, Building a Virtual Data Grid for Gravitational Wave Scientists.  High Performance Distributed Computing, 2002. HPDC-11 2002. Page(s): 225-234.

Book Chapters discussing Pegasus.

Gideon Juve and Ewa Deelman, in Grids, Clouds and Virtualization, M. Cafaro and G. Aloisio, Eds.   Scientific Workflows in the Cloud.  Springer, pp. 71-91, 2010.

Ewa Deelman, Gaurang Mehta, Gurmeet Singh, Mei-Hui Su, and Karan Vahi.  Pegasus: Mapping Large-Scale Workflows to Distributed Resources.  In Workflows for e-Science, 2007.

G. Bruce Berriman, Ewa Deelman, John Good, Joseph C. Jacob, Daniel S. Katz, Anastasia C. Laity, Thomas A. Prince, Gurmeet Singh, and Mei-Hui Su.  Generating Complex Astronomy Workflows.  In Workflows for e-Science, 2007

Philip Maechling, Ewa Deelman, Li Zhao, Robert Graves, Gaurang Mehta, Nitin Gupta, John Mehringer, Carl Kesselman, Scott Callaghan, David Okaya, Hunter Francoeur, Vipin Gupta, Yifeng Cui, Karan Vahi, Thomas Jordan, and Edward Field.  SCEC CyberShake Workflows - Automating Probabilistic Seismic Hazard Analysis Calculations.   In Workflows for e-Science, 2007

Some Ideas about General Workflow Management Architectures

Ewa Deelman, Ian Foster, Carl Kesselman, Reagan Moore, Sanjay Ranka.  Overall Architecture and Control Flow.  GriPhyN technical report 2004-24, December 2003.

This technical report gives an overview of a new architecture being discussed within GriPhyN. This architecture formalizes the workflow generation, refinement and execution processes as graph manipulation (editing) processes.

James Blythe, Richard Cavanaugh, Ewa Deelman, Ian Foster, Seung-Hye Jang, Carl Kesselman, Keith Marzullo, Reagan Moore, Valerie Taylor, Xianan Zhang.  Types of Editors and Specifications.  GriPhyN technical report 2004-23, December 2003.

This report describes the editors that can modify the scientific workflows developed within GriPhyN.

Books on Workflow Technologies

Ian Taylor, Ewa Deelman, Dennis Gannon, and Matthew Shield (Eds.).  Workflows for e-Science.  Springer 2006.

 

 

Presentations

Tutorials

2014

"Pegasus WMS: Enabling Large Scale Workflows on National Cyberinfrastructure" Karan Vahi, Ewa Deelman, Gideon Juve, Mats Rynge, Rajiv Mayani, Rafael Ferreira da Silva. XSEDE 2014, Atlanta, Georgia. July 2014.

2013

"Conducting Large-Scale Imputation Studies on the Cloud" Steven Buyske, Karan Vahi, Ewa Deelman, Ulrike Peters, Tara Matise. ASHG 2013, Boston , Masachuessets, Oct 2013
 
"Pegasus WMS: Enabling Large Scale Workflows on National Cyberinfrastructure"  Karan Vahi, Ewa Deelman, Gideon Juve, Mats Rynge, Rajiv Mayani, Scott Callaghan, Phil Maechling . XSEDE 2013, San Diego, California. July 2013.
 
"Introducing PRECIP - Pegasus Repeatable Experiments for the Cloud in Python" .  Sepideh Azaroosh, Mats Rynge, Gideon Juve,  Ewa Deelman, XSEDE 2012, San Diego, California. July 2013.
 
"Bosco - A simple interface for managing jobs on both XSEDE and campus computing resources" Derek Weitzel, Dan Fraser, Miha Ahronovitz, Mats Rynge, XSEDE 2012, San Diego, California. July 2013.

2012

Curating genomic epidemiology data in The PAGE Study. Gowri Kumaraguruparan, Gaurang Mehta, Andrew Nato, Jose Luis Ambite, Steve Buyske, Rajiv Mayani, Congxing Cai, Jens Vöckler, Ewa Deelman, Tara Matise. ASHG 2012, San Francisco, California Nov 2012

RseqFlow: Workflows for RNA-Seq data analysis. Ying Wang, Gaurang Mehta , Rajiv Mayani ,Tade Souaiaia , Yangho Chen, Andrew Clark , Lin Wan, Oleg V. Evgrafov, James A. Knowles , Ewa Deelman, Ting Chen. ISMB 2012, Long Beach, California  July 2012.

Enabling Bioinformatics Workflows on Leadership Class Systems with Virtual Machines. Gaurang Mehta, Tade Souaiaia, Rajiv Mayani, Ying Wang, Ewa Deelman, Ting Chen and James Knowles. XSEDE 2012, Chicago, Illinois. July 2012.

Pegasus WMS: Enabling Large Scale Workflows on National Cyberinfrastructure. Karan Vahi, Ewa Deelman, Gideon Juve, Gaurang Mehta, Mats Rynge, Rajiv Mayani, Scott Callaghan, Phil Maechling . XSEDE 2012, Chicago, Illinois. July 2012.

Leveraging Pegasus 4.0 and GlideinWMS for Data Intensive Workflows on OSG Karan Vahi, Ewa Deelman, Gideon Juve, Gaurang Mehta, Mats Rynge, Rajiv Mayani, Scott Callaghan, Phil Maechling . OSG All Hands Meeting 2012, Lincoln, Nebraska. March 2012.

2011

Pegasus WMS: Enabling Bioinformatics using Workflow Technologies. G. Mehta, E. Deelman, K. Vahi, Y. Wang, A. Clark, R. Mayani, T. Chen, J. Knowles, #936W Presented at the 12th International Congress of Human Genetics/61st Annual Meeting of The American Society of Human Genetics, October 12, 2011, Montreal, Canada

Generating Large Scale pedigree drawings for Genetic Studies. R. Mayani, G. Mehta, E. Deelman, K. Seth, J. Vöckler, F. Wang, #919W Presented at the 12th International Congress of Human Genetics/61st Annual Meeting of The American Society of Human Genetics, October 12, 2011, Montreal, Canada.

Stampede: A Framework for Monitoring and Troubleshooting of Large-Scale Applications on National Cyberinfrastructure. Fabio Silva, Christopher Brooks, Ewa Deelman, Monte Goode, Dan Gunter, Gideon Juve, Gaurang Mehta, Priscilla Moraes, Taghrid Samak, Martin Swany, Prasanth Thomas, Karan Vahi, Presented at the Teragrid 2011 Conference in Salt Lake City, Utah, July 2011.

2007

TG 2007 - Teragrid Pegasus Poster ppt

2006

SCEC 2006 - SCEC Poster shown at the Annual SCEC Meeting ppt pdf

2005

SC 2005 Pegasus Handout

2004

SC 2004 Pegasus Poster

SC 2004 Pegasus Applications Poster

SC 2004 Pegasus and Applications Handout

SCEC 2004 SCEC Poster shown at the Annual SCEC Meeting

2003

SC 2003 Pegasus and Applications Handout

SC 2003 Pegasus Poster

2002

SC 2002 LIGO and GriPhyN demo Handout

SC 2002 Pegasus and Ligo Data Grid Poster