Collaboration and Sharing


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Presented by Carole Goble at the JISC Future of Research Conference, 19th October 2010

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Collaboration and Sharing

  1. 1. Collaboration and sharing computational research methods Carole Goble University of Manchester, UK
  2. 2. Materials Scientific research is + generally held to be of good provenance when Methods it is documented in + detail sufficient to allow reproducibility. Results = Publication
  3. 3. In silico Experimental Standard Operating, Procedures, Protocols, Plans
  4. 4. E. Science laboris: in silico experiments Automated, reusable scripted analysis pipelines - workflows Data processing , data chaining Data and tool integration Annotation pipelines Analytics Simulation steering and parameter sweeps Publication mining Model and hypothesis building Result Validation and comparison Data cleaning, curation and preservation Shield from clouds and clusters details. Record provenance: steps, methods, results
  5. 5. Genetic variation in cattle species. Food security, biodiversity. Resistance to African trypanosomiasis infection (sleeping sickness) Liverpool (Kemp), Manchester (Brass), Nairobi Comparing new data with reference genomes, prior results and the literature to identifying interesting differences 22 million SNPs
  6. 6. Little Science + Big Science
  7. 7. Bottom up Effectiveness in Research • Automated, repeatable, tracked plumbing – Using institutional and community computing infrastructures, tools and datasets • Easier access to best of breed and “surfing” results – non-developers access to sophisticated codes and applications, shielded from nasty computing details. • Leverage applications, services, datasets and codes shielded from computing details. – Honors original codes and applications. Heterogeneous coding styles and tools sets. The best applications. • Extensibility, adaptability & innovation. – My stuff. Variant design.
  8. 8. Reuse, Recycle, Repurpose, Mash, Trade, Publish Identify biological pathways implicated in resistance to Trypanosomiasis in cattle using mouse as a model organism. Fisher P, et al Nucleic Acids Research, 2007, 35(16) 5625-5633 Dr Paul Fisher Dr Jo Pennock Identify the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the whipworm parasite. Levison S.E., et al Inflammatory Bowel Diseases (2010)
  9. 9. Global Long Tail
  10. 10. How do I find and share methods across the institution, communities, the web ? How do I connect with other authors and users? How do I know if its any good or right for me? Who else is using it? Where do I comment on my experiences?
  11. 11. • Socially share, discover, review and reuse workflows and other scientific methods. • Cooperative market place. • A scientific gateway. • Commons-based Production + Social networking • Primary contribution, reviewing and curating.
  12. 12. Find experts and peers, advice, work flows, packs Contribute, review and curate workflows Train and educate Launch workflows Cloud Methods Commons
  13. 13. Facts and Figures: Boutique but Beautiful • Public Service: 1325 workflows, 349 files, 138 packs, 4129 registered members, 235 groups, 56 different countries, ~ 3000 unique hits per month. Workflows viewed/downloaded many 1000s of times. • Adopted by 19 workflow systems and integrated into workflow workbenches: Galaxy, Taverna – Biology, chemistry, image analysis, social science, astronomy, engineering, music… – Specialised clones in Music & NeuroScience. – Focus of research on workflow patterns and analytics. • JISC funding since 2007 • (Other funding: Microsoft, EU, EPSRC, BBSRC)
  14. 14. Effectiveness and Open Collaboration Open platform, off the shelf components, open development, open linked data, Web 3.0 funky Google gadgets Application plugins Linked Data Cloud
  15. 15. Workbench Gadgets Publishing LogBook Images Software Presentations Literature Compute resources Backup and Archive Friends, colleagues, resources [Duncan Hull] Data (files, spreadsheets)
  16. 16. Workflow management system Collaboration, acceleration and transparency through Automated Computation. Social collaboration environments (“e-Laboratories”) Collaboration, acceleration and transparency through Human Computation
  17. 17. Institutional challenges Adoption of Reproducible Methods New Publishing and Learning Objects Pre-and Post Publication Metadata Differentials Citation, Credit and Reputation Curation Costs
  18. 18. Methods Matter Science 2010 Reproducible (or at least defendable) Research many eyes
  19. 19. Virtual Learning Actionable scholarly Environment publishing & Undergraduate Students learning Digital Libraries scientists Graduate Students Reprints Peer- Reviewed Technical experimentation Journal & Conference Preprints Reports & Papers Metadata Local Web Data, Metadata Repositories Provenance Certified Experimental Workflows Results & Analyses Ontologies [De Roure]
  20. 20. Actionable Compound Research Objects
  21. 21. Data and Method burial Supplementary information Text mining The rise of the Wiki
  22. 22. Competitive advantage. Trust Rewards Adoption. Credit. Help. Fame. Reputation. Being scooped. Risks Scrutiny. Misinterpretation. Cost. Blame. Reputation. Nature 461, 145 (10 September 2009)
  23. 23. Sharing Governance …. “Its not ready yet” “I need to get (another) publication first” “We don’t have the resources or skills to prepare it for others, esp. now we finished that project” “Others won’t use it properly.” “Its not worth my while” “Its faster/easier to do it myself, and will get the credit/control too” “Its not described enough to be usable” “I don’t trust the quality. Its not reliable enough. Its too noisy.
  24. 24. Provenance Credit & Reputation Quality & Reassurance
  25. 25. Crowd Contribution Credit Reward Career Use Profiles Citation Method Building too. Nature 2008
  26. 26. Credit and Reputation Community building T Shirts are not enough Coordination Governance QUALITY for REUSE Sustainability Software Social & Cultural Automation
  27. 27. Public Service Open Software Community generated and curated Content Dig Library/Repository Social network Collaboration platform Computer science research Software engineering Teaching aid Computational researchers Methodology Researchers Social Science Social experiment
  28. 28. Free like puppies
  29. 29. Take Home: Methods Matter. • Workflows are a transformative mechanism of connecting tools and encoding know-how – Scientists stand on the shoulders of resource experts • myExperiment is a example of a collaborative environment for connecting workflow authors and users – Authors stand on the shoulders of each other • The Power of Collectivism. • Rewards and risks of researchers in competitive research. • Cultural shift in reward, adoption and support for building, sharing and curating computational methods.
  30. 30. Acknowledgements myExperiment Director: David De Roure Developers Users Sponsors • Jiten Bhagat • Katy Wolstencroft • Savas Parastatidis • Don Cruickshank • Paul Fisher • Roger Barga • Danius Michaelides • Duncan Hull • Derick Campbell • David Newman • Franck Tanoh • Tony Hey • Sergejs Aleksejevs • Andrea Wiggins • Mark Borkum • Marco Roos • Matt Lee • Jerzy Orlowski • Tom Foster • Olga Krebs • Wolfgang Mueller Allied, Contributing Projects • Tony Linde • Thomas Laurent • Eric Nzuobontane Social Scientists • Ian Dunlop • Yuiwei Lin • Stuart Owen • Rob Proctor • Shoaib Sufi • Meik Poschen • Sean Bechhofer • Jonathan Foster • Rodrigo Lopez • Steve Pettifer • Mannie Tags • Finn Bacall • Sarah Thew • Matt Gamble • Tim Clark
  31. 31. Contact David De Roure Carole Goble Visit