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  • Not just collaboration in workflows, but collaborating with sharing workflows Over 400 taverna workflows publicly available. Combine different formalisms in one system? E.g. a dataflow Kahn network and a central- clock based calculus Kepler logo
  • PPT

    1. 1. Accelerating Time to Experiment – The myExperiment Approach to Open Science David De Roure Carole Goble Jiten Bhagat
    2. 2. 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
    3. 3. <ul><li>What is it? </li></ul><ul><li>How we built it </li></ul><ul><li>Towards the e-Laboratory </li></ul>
    4. 4. <ul><li>What is it? </li></ul>
    5. 5. Taverna Trident Kepler Triana BPEL Ptolemy II
    6. 6. <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
    7. 7. myExperiment.org 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 www.myexperiment.org to access publicly available content or create an account </li></ul>myExperiment.org is... myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs
    8. 15. myExperiment.org 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
    9. 16. Ownership and Attribution The most important aspect of myExperiment Designed by scientists
    10. 17. 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>
    11. 20. <ul><li>How we built it </li></ul>
    12. 21. 24/5/2007 | myExperiment | Slide
    13. 22. 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
    14. 23. 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 myexperiment.org web site is downloadable so you can run your own myExperiment – perhaps for your own lab or projects </li></ul><ul><li>Go to wiki.myexperiment.org for information about our Developer Community </li></ul>
    15. 24. Google Gadgets Bringing myExperiment to the iGoogle user
    16. 25. Taverna Plugin Bringing myExperiment to the Taverna user
    17. 26. Facebook
    18. 27. Silverlight
    19. 28. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX myexp: <http://rdf.myexperiment.org/ontology#> PREFIX sioc: <http://rdfs.org/sioc/ns#> select ?friend1 ?friend2 ?acceptedat where {?z rdf:type <http://rdf.myexperiment.org/ontology#Friendship> . ?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
    20. 30. <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. 31. <ul><li>Towards the e-Laboratory </li></ul>
    22. 33. Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job Execution Naming and Identity Anonymisation Text Mining e-Lab Services
    23. 34. Research Objects
    24. 35. 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, ... </li></ul></ul><ul><li>We are targetting how we believe research will be conducted in the future </li></ul><ul><li>Research Objects are emerging </li></ul>
    25. 36. <ul><li>Contact </li></ul><ul><li>David De Roure </li></ul><ul><li>dder@ecs.soton.ac.uk </li></ul><ul><li>Carole Goble </li></ul><ul><li>[email_address] </li></ul><ul><li>Thanks </li></ul><ul><li>The myGrid Family, National Centre for e-Social Science, CombeChem, Scientific Workflow Community </li></ul>

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