Conceptual-level workflow modeling of scientific experiments using NMR as a case study

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Verdi, Kacy K ^a   Ellis, Heidi J C ^b   Gryk, Michael R ^c  

^a Rensselaer Polytechnic Institute   (United States)

^b TRINITY COLLEGE   (United States)

^c UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR ANALYSIS; BIOMOLECULAR STRUCTURES; INTERMEDIATE RESULTS; NUCLEAR MAGNETIC RESONANCE(NMR); SCIENTIFIC EXPERIMENTS; SCIENTIFIC WORKFLOWS; SEMANTIC MISMATCHES; WORKFLOW IMPLEMENTATIONS;

BIOINFORMATICS; DATA TRANSFER; EXPERIMENTS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SEMANTICS;

DATA FLOW ANALYSIS;

ACCURACY; ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; CONCEPT FORMATION; EXPERIMENTATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OSCILLATION; TIME; VALIDATION STUDY; DECISION SUPPORT SYSTEM; DOCUMENTATION; LABORATORY; NONBIOLOGICAL MODEL; ORGANIZATION AND MANAGEMENT; PROCEDURES; RESEARCH; SCIENCE; WORKPLACE;

DECISION SUPPORT TECHNIQUES; DOCUMENTATION; LABORATORIES; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, ORGANIZATIONAL; RESEARCH; SCIENCE; SOFTWARE; WORKPLACE;

EID: 33847138132     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-31     Document Type: Article

References (33)

1. Altintas I Berkley C Jaeger M Jones M Ludascher B Mock S Kepler: An Extensible System for Design and Execution of Scientific Workflows Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM'04) 2004 1-2
2. Chagoyen M Kurul ME Alarco'n PAD Carazo JM Jupta A Designing and executing scientific workflows with a programmable integrator Bioinformatics 2004 20 13 2092-2100 15059834
3. Medeiros CB Perez-Alcazar J Digiampietri L Pastorello GZ Jr Santanche A Torres RS Madeira E Bacarin E WOODSS and the Web: Annotating and Reusing Scientific Workflows SIGMOD Record 2005 34 3 18-23
4. Ludäscher B Altintas I Berkley C Higgins D Jaeger-Frank E Jones M Lee E Tao J Zhao Y Scientific Workflow Management and the Kepler System Concurrency and Computation: Practice & Experience 2006 18 10 1039-1065
5. Delaglio F Grzesiek S Vuister GW Zhu G Pfeifer J Bax A NMRPipe: A multidimensional spectral processing system based on UNIX pipes J Biomol NMR 1995 6 277-293 8520220
6. Ambler SW Constantine LL The Unified Process Inception Phase: Best Practices for Completing the Unified Process Lawrence: CMP Books 2000
7. Ellis HJC Fox-Erlich S Martyn TO Gryk MR Development of an Integrated Framework for Protein Structure Determinations: A Logical Data Model for NMR Data Analysis Proceedings of the Third International Conference on Information Technology: New Generations (ITNG 2006) 2006 613-618
8. Fox-Erlich S Martyn TO Ellis HJC Gryk M Delineation and Analysis of the Conceptual Data Model Implied by the IUPAC Recommendations for Biochemical Nomenclature Protein Science 2004 13 2559-2563 15295113
9. Oinn T Greenwood M Addis M Alpdemir MN Ferris J Glover K Goble C Goderis A Hull D Marvin D Li P Lord P Pocock MR Senger M Stevens R Wipat A Wroe C Taverna: Lessons in creating a workflow environment for the life sciences Concurrency and Computation: Practice and Experience 2005 18 10 1067-1100
10. Taylor I Shields M Wang I Harrison A Visual Grid Workflow in Triana Journal of Grid Computing 2005 3 3-4 153-169
11. Bowers S Ludäscher B Actor-Oriented Design of Scientific Work-flows Lecture Notes in Computer Science 2005 3716 369-384
12. Kaster DS Medeiros CB Rocha HV Supporting modeling and problem solving from precedent experiences: The role of workflows and case-based reasoning Environmental Modeling & Software 2005 20 6 689-704
13. Seffino LA Medeiros CB Rocha HV Yi B WOODSS - a spatial decision support system based on workflows Decision Support Systems 1999 27 1-2 105-123
14. Oinn T Addis M Ferris J Marvin D Senger M Greenwood M Carver T Glover K Pocock MR Wipat A Li P Taverna: A tool for the composition and enactment of bioinformatics workflows Bioinformatics 2004 20 17 3045-3054 15201187
15. Taylor I Shields M Wang I Ran O Triana Applications within Grid Computing and Peer to Peer Environments Journal of Grid Computing 2003 1 2 199-217
16. Churches D Gombas H Harrison A Maassen J Robinson C Shields M Taylor I Wang I Programming scientific and distributed workflow with Triana services Concurrency and Computation: Practice and Experience 2005 18 10 1021-1037
17. Shankar S Kini A DeWitt DJ Naughton J Integrating databases and workflow systems SIGMOD Record 2005 34 3 5-11
18. Fahringer T Pllana S Villazon A A-GWL: Abstract Grid Workflow Language Lecture Notes in Computer Science 2004 3038 42-49
19. Zhao Y Dobson J Foster I Moreau L Wilde M A Notation and System for Expressing and Executing Cleanly Typed Workflows on Messy Scientific Data SIGMOD Record 2005 34 3 37-43
20. Störrle H Semantics and Verification of Data Flow in UML 2.0 Activities Electronic Notes in Theoretical Computer Science 2005 127 4 35-54
21. Wohed P van der Aalst WMP Dumas M ter Hofstede AHM Russell N Pattern-based Analysis of UML Activity Diagrams BETA Working Paper Series WP 129 Eindhoven University of Technology 2004
22. Bowers S Ludäscher B An Ontology-Driven Framework for Data Transformation in Scientific Workflows Lecture Notes in Computer Science 2004 2994 1-16
23. Berkley C Bowers S Jones M Ludäscher B Schildhauer M Tao J Incorporating Semantics in Scientific Workflow Authoring Proceedings of the 17th International Conference on Scientific and Statistical Database Management (SSDBM'05) 2005 75-78
24. Pathak J Caragea D Honavar VG Ontology-Extended Component-Based Workflows: A Framework for Constructing Complex Workflows from Semantically Heterogeneous Software Components Lecture Notes in Computer Science 2005 3372 41-56
25. Peleg M Tu S Mahindroo A Altman RB Modeling and analyzing biomedical processes using Work-flow/Petri Net models and tools Proc MedInfo 2004 74-78
26. Peleg M Rubin D Altman RB Using Petri Net Tools to Study Properties and Dynamics of Biological Systems Journal of the American Medical Informatics Association 2005 12 2 181-199 551550 15561791
27. Chin G Schuchardt K Myers J Gracio D Participatory Workflow Analysis: Unveiling Scientific Research Processes with Scientists Proceedings of the Sixth Biennial Participatory De-sign Conference 2000
28. Castro AG Thoraval S Garcia LJ Ragan MA Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator BMC Bioinformatics 2005 6 87 1090554 15813976
29. Hollingsworth D The Workflow Reference Model: 10 Years On, The Workflow Handbook 2004 Workflow Management Coalition 2004 295-312
30. Wiegers KE Software Requirements Redmond: Microsoft Press Second 2003
31. Chang RY Continuous Process Improvement San Franciso: Jossey-Bass/ Pfeiffer 1994
32. Galloway D Mapping Work Processes ASQ Quality Press 1994
33. The CONNJUR Project http://www.connjur.org