Workflows for e-Science

1. Front Matter

   Pages i-xxi

   PDF

2. Introduction

   1. Introduction

      • Dennis Gannon, Ewa Deelman, Matthew Shields, Ian Taylor

      Pages 1-8

3. Scientific versus Business Workflows

   1. Scientific versus Business Workflows

      • Roger Barga, Dennis Gannon

      Pages 9-16

4. Application and User Perspective

   1. Front Matter

      Pages 17-17

      PDF

   2. Generating Complex Astronomy Workflows

      • G. Bruce Berriman, Ewa Deelman, John Good, Joseph C. Jacob, Daniel S. Katz, Anastasia C. Laity et al.

      Pages 19-38

   3. A Case Study on the Use of Workflow Technologies for Scientific Analysis: Gravitational Wave Data Analysis

      • Duncan A. Brown, Patrick R. Brady, Alexander Dietz, Junwei Cao, Ben Johnson, John McNabb

      Pages 39-59

   4. Workflows in Pulsar Astronomy

      • John Brooke, Stephen Pickles, Paul Carr, Michael Kramer

      Pages 60-79

   5. Workflow and Biodiversity e-Science

      • Andrew C. Jones

      Pages 80-90

   6. Ecological Niche Modeling Using the Kepler Workflow System

      • Deana D. Pennington, Dan Higgins, A. Townsend Peterson, Matthew B. Jones, Bertram Ludäscher, Shawn Bowers

      Pages 91-108

   7. Case Studies on the Use of Workflow Technologies for Scientific Analysis: The Biomedical Informatics Research Network and the Telescience Project

      • Abel W. Lin, Steven T. Peltier, Jeffrey S. Grethe, Mark H. Ellisman

      Pages 109-125

   8. Dynamic, Adaptive Workflows for Mesoscale Meteorology

      • Dennis Gannon, Beth Plale, Suresh Marru, Gopi Kandaswamy, Yogesh Simmhan, Satoshi Shirasuna

      Pages 126-142

   9. SCEC CyberShake Workflows—Automating Probabilistic Seismic Hazard Analysis Calculations

      • Philip Maechling, Ewa Deelman, Li Zhao, Robert Graves, Gaurang Mehta, Nitin Gupta et al.

      Pages 143-163

5. Workflow Representation and Common Structure

   1. Front Matter

      Pages 165-165

      PDF

   2. Control- Versus Data-Driven Workflows

      • Matthew Shields

      Pages 167-173

   3. Component Architectures and Services: From Application Construction to Scientific Workflows

      • Dennis Gannon

      Pages 174-189

   4. Petri Nets

      • Andreas Hoheisel, Martin Alt

      Pages 190-207

   5. Adapting BPEL to Scientific Workflows

      • Aleksander Slominski

      Pages 208-226

   6. Protocol-Based Integration Using SSDL and π-Calculus

      • Simon Woodman, Savas Parastatidis, Jim Webber

      Pages 227-243

   7. Workflow Composition: Semantic Representations for Flexible Automation

      • Yolanda Gil

      Pages 244-257

   8. Virtual Data Language: A Typed Workflow Notation for Diversely Structured Scientific Data

      • Yong Zhao, Michael Wilde, Ian Foster

      Pages 258-275

This collection of articles on ‘Work?ows for e-Science’ is very timely and - portant. Increasingly, to attack the next generation of scienti?c problems, multidisciplinary and distributed teams of scientists need to collaborate to make progress on these new ‘Grand Challenges’. Scientists now need to access and exploit computational resources and databases that are geographically distributed through theuseof high speed networks. ‘Virtual Organizations’ or ‘VOs’ must be established that span multiple administrative domains and/or institutions and which can provide appropriate authentication and author- ation services and access controls to collaborating members. Some of these VOsmayonlyhavea?eetingexistencebutthelifetimeofothersmayrun into many years. The Grid community is attempting to develop both sta- ards and middleware to enable both scientists and industry to build such VOs routinely and robustly. This, of course, has been the goal of research in distributed computing for many years; but now these technologies come with a new twist service orie- ation. By specifying resources in terms of a service description, rather than allowing direct access to the resources, the IT industry believes that such an approach results in the construction of more robust distributed systems. The industry has therefore united around web services as the standard technology toimplementsuchserviceorientedarchitecturesandtoensureinteroperability between di?erent vendor systems.

• BPEL
• Condor
• DAG
• Grid
• Jini
• Jxta
• OGSA
• OGSI
• Workflow Management
• complexity
• distributed systems
• e-Science
• modeling
• petri net
• programming
• algorithm analysis and problem complexity

• School of Computer Science, Cardiff University, UK

  Ian J. Taylor

• The Center for Computation and Technology, Louisiana State University, USA

  Ian J. Taylor

• Information Sciences Institute, University of Southern California, USA

  Ewa Deelman

• Department of Computer Science, Indiana University, USA

  Dennis B. Gannon

• Schools of Computer Science, Physics and Astronomy, Cardiff University, UK

  Matthew Shields

Dr. Ian Taylor has been a Lecturer at Cardiff University's School of Computer Science since 2002. He concurrently holds an adjunct Assistant Professorship at the Center for Computation & Technology at Louisiana State University and regularly offers consultations in the USA. He has a Ph.D. in Physics and Music and is the co-ordinator of Triana activities at Cardiff (http://www.trianacode.org). Through this he has been active in many major projects including GridLab, CoreGrid and GridOneD. His research interests include distributed techniques and workflow for Grid and P2P computing, which take in applications ranging from astrophysics and healthcare to distributed audio.

Ian has previously written a professional book for Springer on P2P, Web Services and Grids, and has published over 50 scientific papers. He has also co-edited a special edition for Journal of Grid Computing on Scientific Workflow.

Dr. Matthew Shields has been a research associate at Cardiff University, jointly in the Schools of Computer Science,
Physics and Astronomy, since 2001. He gained his Ph.D. in Computer Science from Cardiff University in the area of
problem solving environments. Dr Shields is one of two lead developers for the Triana project and has been responsible
for helping broaden its adoption within new application domains including biodiversity. His interests include problem
solving environments, workflow, component and service based computing, Grid and high-performance computing.

Ewa Deelman is an Research Assistant Professor at the USC Computer Science Department and a Research Team Leader at the Center for Grid Technologies at the USC Information Sciences Institute. Dr. Deelman's research interests include the design and exploration of collaborative scientific environments based on Grid technologies, with particular emphasis on workflow management as well as the management of large amounts of data and metadata. At ISI, Dr. Deelman is leading the Pegasus project, which designs and implements workflow mapping techniques for large-scale workflows running in distributed environments. Pegasus is being used day-to-day by scientists in a variety of disciplines including astronomy, gravitational-wave physics, earthquake science and many others. Prior to joining ISI in 2000, she was a Senior Software Developer at UCLA conducting research in the area of performance prediction of large-scale applications on high performance machines.

Dr. Deelman received her PhD from Rensselaer Polytechnic Institute in Computer Science in 1997 in the area of parallel discrete event simulation. Dr. Deelman is an Associate Editor responsible for Grid Computing for the Scientific Programming Journal and a chair of the GGF Workflow Management Research Group.

Dennis Gannon, Department of Computer Science, Lindley Hall, Indiana University, Bloomington, IN 47401 (gannon@cs.indiana.edu) Dr. Gannon is a professor of Computer Science in the School of Informatics at Indiana University. He is also Science Director for the Indiana Pervasive Technology Labs. He received his Ph.D. in Computer Science from the University of Illinois in 1980 and his Ph.D. in Mathematics from the University of California in 1974. From 1980 to 1985, he was on the faculty at Purdue University. From 1997-2004 he was Chairman of the Indiana Computer Science Department. His research interests include software tools for high performance parallel and distributed systems and problem solving environments for scientific computation.