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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

Published in: Education, Technology
  • Thank you for sharing this!!
    is there any podcast of the talk available?

    In general, I would make the slides less proliss.
    For example, slide 5, 35, 36: there is too much text, people will find it difficult to read the slides and follow what you are saying at the same time.

    for example, slide 35: you cold put just a bullet point list with the titles in bold, and the rest of the text is not necessary (it is you that you have to explain it).

    Moreover, I think your point on slide 5 is too much simplicistic.
    You can't reuse a workflow for your analysis, just because you met a scientist who told you that the workflow is good.
    A good workflow should ideally be published on a peer review journal, or at least have passed a rigourous testing phase.
    Also, the last statement is too much simplicistic, I would remove it.
    Are you sure you want to  Yes  No
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myExperiment - Defining the Social Virtual Research Environment

  1. 1. myExperiment – Defining the Social Virtual Research Environment David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides and David Newman
  2. 2. <ul><li>What is it? </li></ul><ul><li>How we built it </li></ul><ul><li>Towards the e-Laboratory </li></ul>
  3. 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. 4. Taverna Trident Kepler Triana BPEL Ptolemy II
  5. 5. <ul><li>Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle </li></ul><ul><li>Paul meets Jo. Jo is investigating Whipworm in mouse. </li></ul><ul><li>Jo reuses one of Paul’s workflow without change . </li></ul><ul><li>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. </li></ul><ul><li>Previously a manual two year study by Jo had failed to do this. </li></ul>Reuse, Recycling, Repurposing
  6. 6. is… <ul><li>“ Facebook for Scientists”...but different to Facebook! </li></ul><ul><li>A community social network </li></ul><ul><li>Fine control over sharing </li></ul><ul><li>A federated repository </li></ul><ul><li>A gateway to other publishing environments </li></ul><ul><li>A platform for launching workflows </li></ul><ul><li>Started March 2007 </li></ul><ul><li>Closed beta since July 2007 </li></ul><ul><li>Open beta November 2007 </li></ul><ul><li>Go to to access publicly available content or create an account </li></ul> is... myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs
  7. 14. is… <ul><li>User Profiles </li></ul><ul><li>Groups </li></ul><ul><li>Friends </li></ul><ul><li>Sharing </li></ul><ul><li>Tags </li></ul><ul><li>Workflows </li></ul><ul><li>Developer interface </li></ul><ul><li>Credits and Attributions </li></ul><ul><li>Fine control over privacy </li></ul><ul><li>Packs </li></ul><ul><li>Federation </li></ul><ul><li>Enactment </li></ul>myExperiment Features Distinctives
  8. 15. Ownership and Attribution The most important aspect of myExperiment Designed by scientists
  9. 16. Packs <ul><li>Packs allow you to collect different items together, like you might with a &quot;wish list&quot; or &quot;shopping basket&quot; </li></ul><ul><li>You can collect internal things (such as workflows, files and even other packs) as well as link to things outside myExperiment </li></ul><ul><li>Your packs can then be shared, tagged, discovered and discussed easily on myExperiment </li></ul>
  10. 18. <ul><li>How we built it </li></ul>
  11. 19. 24/5/2007 | myExperiment | Slide
  12. 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
  13. 21. For Developers <ul><li>All the myExperiment services are accessible through simple RESTful programming interfaces </li></ul><ul><ul><li>use your existing environment and augment it with myExperiment functionality </li></ul></ul><ul><ul><li>build entirely new interfaces and functionality mashups </li></ul></ul><ul><li>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 </li></ul><ul><li>Go to for information about our Developer Community </li></ul>
  14. 22. Google Gadgets Bringing myExperiment to the iGoogle user
  15. 23. Taverna Plugin Bringing myExperiment to the Taverna user
  16. 24. Facebook
  17. 25. Silverlight
  18. 26. Exporting packs
  19. 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
  20. 29. <ul><li>Fit in, Don’t Force Change </li></ul><ul><li>Jam today and more jam tomorrow </li></ul><ul><li>Just in Time and Just Enough </li></ul><ul><li>Act Local, think Global </li></ul><ul><li>Enable Users to Add Value </li></ul><ul><li>Design for Network Effects </li></ul>Six Principles of Software Design to Empower Scientists <ul><li>Keep your Friends Close </li></ul><ul><li>Embed </li></ul><ul><li>Keep Sight of the Bigger Picture </li></ul><ul><li>Favours will be in your Favour </li></ul><ul><li>Know your users </li></ul><ul><li>Expect and Anticipate Change </li></ul>De Roure, D. and Goble, C. (2009) Six Principles of Software Design to Empower Scientists. IEEE Software (in press)
  21. 30. <ul><li>Towards the e-Laboratory </li></ul>
  22. 31. e-Laboratory Lifecycle
  23. 32. Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job Execution Naming and Identity Anonymisation Text Mining Research Object Management Assembling e-Laboratories Example Core Services <ul><li>An e-Lab is a set of components and resources </li></ul><ul><ul><li>An open system, not a software monolith </li></ul></ul><ul><ul><li>Utility of components transcends their immediate application </li></ul></ul><ul><li>We envisage an ecosystem of cooperating e-Laboratories </li></ul><ul><li>What are the e-Lab components and services? </li></ul><ul><li>What are the Research Objects? </li></ul>
  24. 33. Research Objects
  25. 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 Automated refine validate seed Reuse and Symbiosis
  26. 35. <ul><li>It should facilitate the management and sharing of Research Objects – these are the digital commodities that are used and reused by researchers, ranging from data and methods to scholarly publications. </li></ul><ul><li>It should support the social 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- and community-curation. </li></ul><ul><li>It should provide an open, extensible environment to permit ease of integration with other software, tools and services, and benefit from participative contribution of software. </li></ul><ul><li>It should provide a platform to action research , for example to deliver research objects to remote services and software. It should be straightforward to create customised, task specific tools and environments. </li></ul>Defining the Social Virtual Research Environment
  27. 36. Reflections <ul><li>myExperiment provides social infrastructure – it facilitates sharing and enables scientists to collaborate in order to compete </li></ul><ul><li>myExperiment has growing community and growing content </li></ul><ul><ul><li>Supports Taverna, Trident, UsefulChem, ... </li></ul></ul><ul><ul><li>Kepler, Meandre next </li></ul></ul><ul><ul><li>Scale makes discovery more difficult and easier! </li></ul></ul><ul><ul><li>Could share R, matlab, statistical models, spreadsheets </li></ul></ul><ul><li>We are targetting how we believe research will be conducted in the future, through the assembly of e-Laboratories which share Research Objects </li></ul>
  28. 37. <ul><li>Contact </li></ul><ul><li>David De Roure </li></ul><ul><li> </li></ul><ul><li>Carole Goble </li></ul><ul><li>[email_address] </li></ul><ul><li>Further info </li></ul><ul><li> </li></ul><ul><li>Thanks </li></ul><ul><li>The myGrid Family, National Centre for e-Social Science, CombeChem, Scientific Workflow Community </li></ul>