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myExperiment – Defining the Social Virtual Research Environment David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshan...
<ul><li>What is it? </li></ul><ul><li>How we built it </li></ul><ul><li>Towards the e-Laboratory </li></ul>
scientists Graduate Students Undergraduate Students experimentation Data, Metadata Provenance Workflows Ontologies Digital...
Taverna Trident Kepler Triana BPEL Ptolemy II
<ul><li>Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis  in cattle <...
myExperiment.org is… <ul><li>“ Facebook for Scientists”...but different to Facebook! </li></ul><ul><li>A community social ...
 
 
 
 
 
 
 
myExperiment.org is… <ul><li>User Profiles </li></ul><ul><li>Groups </li></ul><ul><li>Friends </li></ul><ul><li>Sharing </...
Ownership and Attribution The most important aspect of myExperiment Designed by scientists
Packs <ul><li>Packs allow you to collect different items together, like you might with a &quot;wish list&quot; or &quot;sh...
 
<ul><li>How we built it </li></ul>
24/5/2007  |  myExperiment  |  Slide
HTML For Developers mySQL Search Engine reviews ratings groups friendships tags Enactor files workflows ` RDF Store SPARQL...
For Developers <ul><li>All the myExperiment services are accessible through simple RESTful programming interfaces  </li></...
Google Gadgets Bringing myExperiment to the iGoogle user
Taverna Plugin Bringing myExperiment to the Taverna user
Facebook
Silverlight
Exporting packs
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX myexp: <http://rdf.myexperiment.org/ontology#> PREFIX sio...
 
<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 Ju...
<ul><li>Towards the e-Laboratory </li></ul>
e-Laboratory Lifecycle
Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job E...
Research Objects
Content Capture and Curation Workflows and Services Experts Social by User Community refine validate refine validate Self ...
<ul><li>It should facilitate the management and sharing of  Research Objects   – these are the digital commodities that ar...
Reflections <ul><li>myExperiment provides social infrastructure – it facilitates sharing and enables scientists to collabo...
<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 </...
 
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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
  • In particular a platform for research into curation practices As in the panel today Expert – Is library like Suppliers and crowd are the web side Automated is Expert curators : bioinformaticians who understand the services and workflows whose job it is to annotate and set up the curation pipelines, for services and workflows that are not of their own making. Self-curation: Some registries are closed – the myGrid registry is only curated by experts from the myGrid project itself. Others encourage service developers to self-curate, emphasising the use of plug-ins to service development environments such as Eclipse; examples include BioMoby’s jMoby plugin and SAWSDL4J, Lumina and Radiant toolkits for SAWSDL and WSMO Studio (21). Workflow repositories such as myExperiment rely on self-curation by the workflow developers and community curation by their users. Challenges include (a) the enforcement of controlled vocabularies by self-curators, particularly if the vocabularies are also managed by the developers as they can quickly become unruly and (b) incentivising people to contribute their services and workflows for the good of the community. Community Curators : The trend is to follow in the footsteps of popular Web 2.0 social computing sites and encourage community curation through user feedback, blogging, e-tracking, recommendations and folksonomy based tagging. Community approach to services development and use being tried by Seekda and BioMoby and for workflows by myExperiment. Community and self-curation requires built-in incentive models for people to contribute such as credit and attribution, but can be made to work for example iCapture successfully pioneered community curation of ontologies (Wilkinson PSB). Automated Curators : Automated scavengers and crawlers identify candidates for submission and extract as much metadata as possible. Functional metadata is hard to auto-curate, requiring: specialist metadata extraction tools [54]; software plug-ins that incidentally gather metadata from services as they are used in applications; or smart reasoning over seeded service descriptions and workflows [54]. Operational and usage metadata is ripe for automation, generated from monitoring services, application diagnostics, customer reports and Social Network Analysis. Workflow analytics is the term used for processing workflow collections to identify, for example, service co-use patterns and service popularity. Automated curation needs excellent infrastructure.
  • Transcript of "PPT"

    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. 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
    7. 14. 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
    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 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>
    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: <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 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>dder@ecs.soton.ac.uk </li></ul><ul><li>Carole Goble </li></ul><ul><li>[email_address] </li></ul><ul><li>Further info </li></ul><ul><li>wiki.myexperiment.org </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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