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The myExperiment approach to Open Science David De Roure Carole Goble Jiten Bhagat Don Cruickshank
scientists Graduate Students Undergraduate Students experimentation Data, Metadata Provenance Workflows Ontologies Digital...
Sharing pieces of process Carole Goble and David De Roure,  Curating Scientific Web Services and Workflows , EDUCAUSE Revi...
myExperiment.org is… <ul><li>“ Facebook for Scientists”...but different to Facebook! </li></ul><ul><li>A community social ...
 
 
 
 
 
“ Do I want my Science associated with a medium like this?”
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...
 
Exporting packs
24/5/2007  |  myExperiment  |  Slide
Google Gadgets Bringing myExperiment to the iGoogle user
Taverna Plugin Bringing myExperiment to the Taverna user
Facebook
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...
e-Laboratory Lifecycle
Workflow Monitoring Event Logging Social Metadata Annotation Service Search User Registration Distributed Data Query Job E...
Content Capture and Curation Workflows and Services Experts Social by User Community refine validate refine validate Self ...
Summary <ul><li>myExperiment provides social infrastructure – it facilitates sharing and enables scientists to collaborate...
<ul><li>Contact </li></ul><ul><li>David De Roure </li></ul><ul><li>dder@ecs.soton.ac.uk  </li></ul><ul><li>http://blog.ope...
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My Experiment

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MyExperiment è un social network all’interno del quale è possibile cercare flussi di lavoro scientifico resi pubblici, ma anche proporre, condividere e svilupparne di nuovi, al fine di creare delle comunità e sviluppare relazioni. La presentazione illustra la visione di My Experiment sull' Open Science

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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 "My Experiment"

    1. 1. The myExperiment approach to Open Science David De Roure Carole Goble Jiten Bhagat Don Cruickshank
    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. Sharing pieces of process Carole Goble and David De Roure, Curating Scientific Web Services and Workflows , EDUCAUSE Review, vol. 43, no. 5 (September/October 2008) http://usefulchem.wikispaces.com/page/code/EXPLAN001 http://www.microsoft.com/mscorp/tc/trident.mspx http://www.mygrid.org.uk/tools/taverna/
    4. 4. 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>Open source (BSD) </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 1400 registered users, 120 groups, 540 workflows, 147 files and 44 packs
    5. 10. “ Do I want my Science associated with a medium like this?”
    6. 11. 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 Distinctives
    7. 12. Ownership and Attribution The most important aspect of myExperiment Designed by scientists
    8. 13. 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>
    9. 15. Exporting packs
    10. 16. 24/5/2007 | myExperiment | Slide
    11. 17. Google Gadgets Bringing myExperiment to the iGoogle user
    12. 18. Taverna Plugin Bringing myExperiment to the Taverna user
    13. 19. Facebook
    14. 20. 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
    15. 22. <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. Software Design for Empowering Scientists, IEEE Software, Volume 26, Issue 1, Jan-Feb 2009, pages 88-95.
    16. 23. e-Laboratory Lifecycle
    17. 24. 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>
    18. 25. 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
    19. 26. Summary <ul><li>myExperiment provides social infrastructure – it facilitates sharing and enables scientists to collaborate in order to compete. Reputation and incentives. </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>Team working on Kepler, Meandre next </li></ul></ul><ul><ul><li>Community added WSVLAM, GWorkflowDL, ... </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>
    20. 27. <ul><li>Contact </li></ul><ul><li>David De Roure </li></ul><ul><li>dder@ecs.soton.ac.uk </li></ul><ul><li>http://blog.openwetware.org/eresearch/ </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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