1 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

2 ESIP meeting,Santa Barbara, CA, July P. Missier Provenance in Taverna: example geneIDspathway s List-structured KEGG gene ids: [ [ mmu:26416 ], [ mmu: ] ] [ path:mmu04010 MAPK signaling, path:mmu04370 VEGF signaling ] geneIDspathway s [ [ path:mmu04210 Apoptosis, path:mmu04010 MAPK signaling,...], [ path:mmu04010 MAPK signaling, path:mmu04620 Toll-like receptor,...] ]

3 ESIP meeting,Santa Barbara, CA, July P. Missier Provenance management architecture Taverna runtime process design Provenance capture component provenance events -input arrived -service invoked -output produced Provenance DB relational data model Lineage query processor workflow results Results browser Results analysis Provenance browser workflow inputs

User Profiles Groups Friends Sharing Tags Workflows Developer interface Credits and Attributions Fine control over privacy Packs Federation Enactment myExperiment Features Distinctives

Packs in Practice

Exporting packs

e-Laboratory Lifecycle Local projects using Taverna and/or myExperiment SysMO Ondex Obesity eLab Shared Genomics NEMA neurohub CombeChem LifeGuide IBBRE myExperimental Science

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 Generation The 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 Paper Slides Feeds into produces Included in produces Published in produces Included in Published in Workflow 16 Workflow 13 Common pathways QTL Paul’s Pack Paul’s Research Object

Communications of the ACM 51, 4 (Apr. 2008), Scientific Discourse Relationships Ontology Specification Open Provenance Model

David Shotton

Contact David De Roure Carole Goble Visit wiki.myexperiment.org

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, Curating Scientific Web Services and Workflows by Carole Goble and David De Roure. EDUCAUSE Review, vol. 43, no. 5 (September/October 2008) 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: /eScience doi: /eScience De Roure, D. and Goble, C. (2009) "Software Design for Empowering Scientists," IEEE Software, vol. 26, no. 1, pp , January/February doi: /MS doi: /MS 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, References