myexperiment - defining the social virtual research environment

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Presented at the 4th IEEE International Conference on e-Science, Indianapolis, December 11, 2008


  • 1. myExperiment Defining the Social Virtual Research Environment David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides and David Newman


  • What is it?
  • How we built it
  • Towards the e-Laboratory

3. scientists Graduate Students Undergraduate Students experimentation Data, Metadata Provenance Workflows Ontologies Digital Libraries The social process of Science 2.0 Local Web Repositories Virtual Learning Environment Technical Reports Reprints Peer-Reviewed Journal & Conference Papers Preprints & Metadata Certified Experimental Results & Analyses 4. Taverna Trident Kepler Triana BPEL Ptolemy II 5.

  • Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasisin cattle
  • Paul meets Jo. Jo is investigating Whipworm in mouse.
  • Jo reuses one of Pauls workflowwithout change .
  • Jo identifies the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the parasite.
  • Previously a manualtwo year studyby Johad failed to do this.

Reuse, Recycling, Repurposing 6. is

  • Facebook for Scientists...but different to Facebook!
  • A community social network
  • Fine control over sharing
  • A federated repository
  • A gateway to other publishing environments
  • A platform for launching workflows
  • Started March 2007
  • Closed beta since July 2007
  • Open beta November 2007
  • Go towww.myexperiment.orgto access publicly available content or create an account is... myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs 7. 8. 9. 10. 11. 12. 13. 14. is

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

myExperiment Features Distinctives 15. Ownership and Attribution The most important aspect of myExperiment Designed by scientists 16. Packs

  • Packs allow you to collect different items together, like you might with a "wish list" or "shopping basket"
  • You can collect internal things (such as workflows, files and even other packs) as well as link to things outside myExperiment
  • Your packs can then be shared, tagged, discovered and discussed easily on myExperiment

17. 18.

  • How we built it

19. 24/5/2007|myExperiment|Slide 20. HTML For Developers mySQL Search Engine reviews ratings groups friendships tags Enactor files workflows ` RDF Store SPARQL endpoint Managed REST API facebook iGoogle android XML API config profiles packs credits 21. For Developers

  • All the myExperiment services are accessible through simple RESTful programming interfaces
    • use your existing environment and augment it with myExperiment functionality
    • build entirely new interfaces and functionality mashups
  • The open source Web 2.0 Software that powers the web site is downloadable so you can run your own myExperiment perhaps for your own lab or projects
  • Go towiki.myexperiment.orgfor information about our Developer Community

22. Google Gadgets Bringing myExperiment to the iGoogle user 23. Taverna Plugin Bringing myExperiment to the Taverna user 24. Facebook 25. Silverlight 26. Exporting packs 27. PREFIX rdf: PREFIX myexp: PREFIX sioc: select ?friend1 ?friend2 ?acceptedat where {?z rdf:type . ?z myexp:has-requester ?x . ?x sioc:name ?friend1 . ?z myexp:has-accepter ?y . ?y sioc:name ?friend2 . ?z myexp:accepted-at ?acceptedat } All accepted Friendships including accepted-at time Semantically-Interlinked Online Communities SPARQL endpoint 28. 29.

  • Fit in, Dont Force Change
  • Jam today and more jam tomorrow
  • Just in Time and Just Enough
  • Act Local, think Global
  • Enable Users to Add Value
  • Design for Network Effects

Six Principles of Software Design to Empower Scientists

  • Keep your Friends Close
  • Embed
  • Keep Sight of the Bigger Picture
  • Favours will be in your Favour
  • Know your users
  • Expect and Anticipate Change

De Roure, D. and Goble, C. (2009) Six Principles of Software Design to Empower Scientists. IEEE Software (in press) 30.

  • Towards the e-Laboratory

31. e-Laboratory Lifecycle 32. Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job Execution Naming and Identity Anonymisation Text MiningResearch Object Management Assembling e-Laboratories Example Core Services

  • An e-Lab is a set of components and resources
    • An open system, not a software monolith
    • Utility of components transcends their immediate application
  • We envisage an ecosystem of cooperating e-Laboratories
  • What are the e-Lab components and services?
  • What are the Research Objects?

33. Research Objects 34. Content Capture and Curation Workflows and Services Experts Social by User Community refine validate refine validate Self by Service Providers seed seed refine validate seed Automatedrefine validate seed Reuse and Symbiosis 35.

  • It should facilitate the management and sharing ofResearch Objects these are the digital commodities that are used and reused by researchers, ranging from data and methods toscholarly publications.
  • It should support thesocial model :producers of research objects should have incentives to make them available; consumers need to be able to discover and reuse them; all will benefit from self- andcommunity-curation.
  • It should provide anopen, extensible environmentto permit ease of integration with other software, tools and services, and benefit from participativecontribution of software.
  • It should provide a platform toaction research , forexample to deliver research objects to remote services and software. It should be straightforward to create customised, task specific tools andenvironments.

Defining the Social Virtual Research Environment 36. Reflections

  • myExperiment provides social infrastructure it facilitates sharing and enables scientists to collaborate in order to compete
  • myExperiment has growing community and growing content
    • Supports Taverna, Trident, UsefulChem, ...
    • Kepler, Meandre next
    • Scale makes discovery more difficult and easier!
    • Could share R, matlab, statistical models, spreadsheets
  • We are targetting how we believe research will be conducted in the future, through the assembly ofe-Laboratories which share Research Objects


  • Contact
  • David De Roure
  • Carole Goble
  • [email_address]
  • Further info
  • Thanks
  • The myGrid Family, National Centre for e-Social Science, CombeChem, Scientific Workflow Community


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