1 dr. paolo missier, prof. carole goble information management group school of computer science,...
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Dr. Paolo Missier, Prof. Carole Goble
Information Management Group
School of Computer Science, University of Manchester, UK
with additional material by:
Prof. Dave DeRoure
Univ. of Southampton, UK
Scientific Workflow Management System
e-Labs, Research Objects, and Provenance
2ESIP meeting,Santa Barbara, CA, July 2009 - P. Missier
Provenance in Taverna: example
geneIDs pathways
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List-structured KEGG gene ids:
[ [ mmu:26416 ], [ mmu:328788 ] ]
[ path:mmu04010 MAPK signaling, path:mmu04370 VEGF signaling ]
geneIDs pathways
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[ [ path:mmu04210 Apoptosis, path:mmu04010 MAPK signaling, ...], [ path:mmu04010 MAPK signaling , path:mmu04620 Toll-like receptor, ...] ]
3ESIP meeting,Santa Barbara, CA, July 2009 - P. Missier
Provenance management architecture
Tavernaruntime
processdesign
Provenance capture
component
provenance events-input arrived-service invoked-output produced
ProvenanceDB
relationaldata model
Lineagequery
processor
workflowresults
Results browser
Results analysis
Provenance browser
workflowinputs
User ProfilesGroupsFriendsSharingTagsWorkflowsDeveloper interfaceCredits and AttributionsFine control over privacyPacksFederationEnactment
myExperiment FeaturesD
istin
ctiv
es
Packs in Practice
Exporting packs
e-Laboratory Lifecycle Local projects using Taverna and/or myExperiment
SysMOOndexObesity eLabShared GenomicsNEMAneurohubCombeChemLifeGuideIBBREmyExperimentalScience
1st Generation
Current practice of early adoptors of e-Labs tools such as Taverna, ELNs, LIMS.
Characterised by researchers using tools within their particular problem area, with some re-use of tools, data and methods within the discipline.
Traditional publishing is supplemented by publication of some digital items like workflows and links to data.
Provenance is recorded but not shared and re-used.
Science is accelerated and practice beginning to shift to emphasise in silico work.
e-Laboratory Evolution
2nd Generation
Designing and delivering now, based on experience with Taverna, myExperiment and Lablogs.
Key characteristic is re-use - of the increasing pool of tools, data and methods, across areas & disciplines.
Contain some freestanding, recombinant, reproducible Research Objects.
Provenance analytics plays a role.
Expert curation supplemented by community curation.
New scientific practices are established and opportunities arise for completely new scientific investigations.
3rd GenerationThe vision - the e-Labs we'll be delivering in 5 years - illustrated by open science and open source science.Characterised by global reuse of tools, data and methods across any discipline, and surfacing the right levels of complexity for the researcher. Key characteristic is radical sharing Research is significantly data driven - plundering the backlog of data, results and methods. Research Objects supersede papers.Increasing automation and decision-support for the researcher - the e-Laboratory becomes assistive. Provenance assists design.Curation is autonomic and social.Entirely new research outcomes are obtained.
Results
Logs
Results
Metadata PaperSlides
Feeds into
produces
Included in
produces Published in
produces
Included in
Included in Included in
Published in
Workflow 16
Workflow 13
Common pathways
QTLPaul’s PackPaul’s Research
Object
Communications of the ACM 51, 4 (Apr. 2008), 52-58
Scientific Discourse Relationships Ontology Specification
Open Provenance Model
David Shotton
Allan, R., Allden, A., Boyd, D., Crouchley, R., Harris, N., Lyon, L., Robiette, A., De Roure, D. and Wilson, S. Roadmap for a UK Virtual Research Environment: Report of the JCSR VRE Working Group, JISC, 2004 http://www.jisc.ac.uk/uploaded_documents/VRE%20roadmap%20v4.pdf
Curating Scientific Web Services and Workflows by Carole Goble and David De Roure. EDUCAUSE Review, vol. 43, no. 5 (September/October 2008) http://connect.educause.edu/Library/EDUCAUSE+Review/CuratingScientificWebServ/47226
De Roure, D., Goble, C., Bhagat, J., Cruickshank, D., Goderis, A., Michaelides, D. and Newman, D. (2008) myExperiment: Defining the Social Virtual Research Environment. In: 4th IEEE International Conference on e-Science, 7-12 December 2008, Indianapolis, Indiana, USA. doi:10.1109/eScience.2008.86
De Roure, D. and Goble, C. (2009) "Software Design for Empowering Scientists," IEEE Software, vol. 26, no. 1, pp. 88-95, January/February 2009. doi:10.1109/MS.2009.22
Luc Moreau, Juliana Freire, Joe Futrelle, Robert E. McGrath, Jim Myers, Patrick Paulson: The Open Provenance Model: An Overview. IPAW 2008: LNCS 5272, Springer-Verlag , pp. 323–326, 2008.
References