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Accelerating Time to Experiment – The myExperiment Approach to Open Science

Accelerating Time to Experiment – The myExperiment Approach to Open Science. David De Roure Carole Goble Jiten Bhagat. Virtual Learning Environment. Reprints. Peer-Reviewed Journal & Conference Papers. Technical Reports. Local Web. Preprints & Metadata. Repositories.

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Accelerating Time to Experiment – The myExperiment Approach to Open Science

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  1. Accelerating Time to Experiment –The myExperiment Approach to Open Science David De Roure Carole Goble Jiten Bhagat

  2. Virtual Learning Environment Reprints Peer-Reviewed Journal & Conference Papers Technical Reports LocalWeb Preprints & Metadata Repositories Certified Experimental Results & Analyses The social process of Science 2.0 Undergraduate Students Digital Libraries scientists Graduate Students experimentation Data, Metadata Provenance WorkflowsOntologies

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

  4. What is it?

  5. Kepler Ptolemy II Triana BPEL Trident Taverna

  6. Reuse, Recycling, Repurposing • Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle • Paul meets Jo. Jo is investigating Whipworm in mouse. • Jo reuses one of Paul’s workflow without 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 manual two year study by Jo had failed to do this.

  7. myExperiment.org is… myExperiment.org 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 to www.myexperiment.org to access publicly available content or create an account myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs

  8. myExperiment.org is… myExperiment Features • User Profiles • Groups • Friends • Sharing • Tags • Workflows • Developer interface • Credits and Attributions • Fine control over privacy • Packs • Federation • Enactment

  9. Ownership and Attribution The most important aspect of myExperiment Designed by scientists

  10. 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

  11. How we built it

  12. For Developers XML ORE FOAF SIOC facebook iGoogle android APIconfig HTML SearchAPI Managed REST API Search Engine SPARQL endpoint tags ratings reviews profiles groups workflows credits EPrints DSpace Fedora S3 SRB friendships packs files ` RDF Store mySQL Enactor API Enactor

  13. 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 myexperiment.org web site is downloadable so you can run your own myExperiment – perhaps for your own lab or projects • Go to wiki.myexperiment.org for information about our Developer Community

  14. Google Gadgets Bringing myExperiment to the iGoogle user

  15. Taverna Plugin Bringing myExperiment to the Taverna user

  16. Facebook

  17. Silverlight

  18. 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

  19. 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 • Fit in, Don’t 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 De Roure, D. and Goble, C. (2009) Six Principles of Software Design to Empower Scientists. IEEE Software (in press)

  20. Towards the e-Laboratory

  21. e-Lab Services Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job ExecutionNaming and Identity Anonymisation Text Mining

  22. Research Objects

  23. 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, ... • We are targetting how we believe research will be conducted in the future • Research Objects are emerging

  24. Contact David De Roure dder@ecs.soton.ac.uk Carole Goble carole.goble@manchester.ac.uk Thanks The myGrid Family, National Centre for e-Social Science, CombeChem, Scientific Workflow Community

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