Bhagat Myexperiment Bosc2008

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  • 1. Jiten Bhagat University of Manchester David De Roure – University of Southampton Carole Goble – University of Manchester Don Cruickshank – University of Southampton Marco Roos – University of Amsterdam www.myexperiment.org myExperiment: social software for sharing workflows
  • 2. Sales Pitch
    • myExperiment makes it really easy for the next generation of scientists to contribute to a pool of scientific workflows, build communities and form relationships. It enables scientists to share, reuse and repurpose workflows and reduce time-to-experiment, share expertise and avoid reinvention.
  • 3. Use myExperiment to… Build packs of related content Share your workflows and files Control access to your workflows and files Find workflows and files that others have shared Maintain and use different versions of workflows Tag and rate workflows and files Write reviews and comments Have discussions and collaborate Create and join groups of similar interests Find people and make friends Send messages to other people on myExperiment Build your profile and reputation
      • Execute workflows directly within myExperiment
      • (if you have access to a remote Taverna enactor)
    Reuse and repurpose workflows (and other files!)
  • 4. Bare Facts
    • 16 months old
    • Built on Ruby on Rails
    • BSD License
    • Source code hosted on RubyForge
      • Publicly available
    • 2 core developers
      • 50% in Southampton, 50% in Manchester
    • User driven design and development
    Mar 2007 – start of project Jul 2007 – closed beta Nov 2007 – open beta
  • 5. Vitals – July 2008
      • 959 active users
      • 1429 unique IP visits in last month
      • 82 groups
      • 248 group memberships
      • 296 workflow entries, 425 workflow versions
      • 101 files
      • 1382 taggings
      • 46,427 downloads
      • 77,393 viewings
      • 408 creditations
      • 12 packs (with 237 total entries)
    myExperiment has over 950 users (over 1400 unique IP visits last month) , 80 groups, 290 workflows, 100 files and 10 packs … with over 46,000 downloads of workflows/files
  • 6. SETTING THE CONTEXT
    • Why do we need an environment like myExperiment?
  • 7. Taverna Workflow Workbench
    • Taverna enables the interoperation between databases and tools by providing a toolkit for composing, executing and managing workflow experiments
    • Access to local and remote resources and analysis tools
    • Automation of data flow
    • Iteration over large data sets
    Part of the myGrid project
  • 8. Who uses Taverna?
    • 350+ organisations
    • 40,000+ downloads
    • Users worldwide
    • Systems biology
    • Proteomics
    • Gene/protein annotation
    • Microarray data analysis
    • Medical image analysis
    • Heart simulations
    • High throughput screening
    • Genotype/Phenotype studies
    • Health Informatics
    • Astronomy
    • Chemoinformatics
    • Data integration
    • ISMB07 – 6 posters, 2 demos,
    • 1 BOF, 1 tutorial
  • 9. Taverna Kepler Triana BPEL Ptolemy II
  • 10. Encapsulating your Experiment
    • Workflows are protocols and records.
      • Explicit and precise descriptions of a scientific protocol
      • Scientific transparency. Easier to explain, share, relocate, reuse and repurpose and remember.
      • Provenance of results for credibility.
    • Workflows are know-how.
      • Specialists create applications; experts design and set parameters; inexperienced punch above their weight with sophisticated protocols
    • Workflows are collaborations.
      • Multi-disciplinary workflows promote even broader collaborations.
  • 11. But…
    • Workflow design is challenging and labour-intensive.
      • Reuse is highly desirable.
    • Reuse is a challenge
      • especially for individuals or small groups, decoupled from each other and acting independently.
      • workflows that cover processes outside of expertise.
      • workflows from a common pool of components.
      • workflows shared across discipline boundaries.
      • when inexperienced scientists need to leverage the expertise of others.
  • 12. Recycling, Reuse, 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.
  • 13. As Taverna’s popularity increased we observed a workflow exchange activity emerging amongst our users and a strong desire for a place were workflows could be collected and opened to peer review.
  • 14.  
  • 15. myExperiment enables scientists to discover , reuse and repurpose workflows, and to enact them from a web page using a remote enactment service.
  • 16.  
  • 17.  
  • 18. Workflow Components
      • See the internals of a workflow
      • Aids decision making when deciding on reuse/repurposing
  • 19.  
  • 20. Workflow Enactment
  • 21.  
  • 22. myExperiment focuses on the special requirements of scientists, providing support for: ownership , credit and attribution , licensing , visibility and sharing .
  • 23. Workflow Upload
  • 24.  
  • 25. Just Enough Sharing….
    • myExperiment can provide a central location for workflows from one community/group
    • myExperiment allows you to say
      • Who can look at your workflow
      • Who can download your workflow
      • Who can modify your workflow
      • Who can run your workflow
  • 26. myExperiment aids reuse because workflows can be discovered not just by what they do but based on how they are used by the community , with tags and reviews adding to the ‘collective intelligence’.
  • 27. Workflows have friends (and social metadata) too!
      • Emphasising social networking around the workflows.
      • Attributions show what workflows/files it’s based on (= reuse/repurpose).
  • 28.  
  • 29. myExperiment is not just about workflows, it’s about sharing digital objects, which include data, results, provenance information, tags, associated documentation, etc. … collected together to form scientific research objects , for example to record an experiment.
  • 30. Packs
  • 31.  
  • 32.  
  • 33. myExperiment functionality can be accessed through simple RESTful APIs so that it can be accessed through existing interfaces, including wikis, web pages… and Taverna. Also enables the creation of other interfaces such as Google Gadgets, myExperiment add-ons for sites such as Facebook and functionality mashups over myExperiment.
  • 34. Google Gadgets
  • 35. Taverna Plugin
    • One click' workflow launch from myExperiment to Taverna (using WHIP).
    • Browse the example workflows mantained and curated by a member of the Taverna team (Alan Williams).
    • Browse the latest workflows from myExperiment.
    • Search for workflows from myExperiment.
    • View a dynamic and resizeable tag cloud from myExperiment.
    • Get workflows based on a tag.
    • 'Preview' a workflow - get more information from myExperiment about a workflow.
    • Open a workflow in design mode (when in the myExperiment section of the plugin).
    • Import a workflow into a current workflow in design mode.
  • 36. myExperiment is an open source codebase (released under the BSD licence). Individuals and laboratories are free to install their own myExperiment instances.
  • 37. Developer Support
    • Anyone can download and set up their own myExperiment - http://rubyforge.org/projects/myexperiment/
    • We have a new wiki to support external developers and their projects – http://wiki.myexperiment.org/
  • 38.  
  • 39. Future
    • Ability to "subscribe" to a workflow or group
      • so that you can be updated whenever something new happens or something is updated (eg: a new comment or new tag is set).
    • Ability to attach documents and data to workflow entries in myExperiment.
    • Uploading Taverna 2, Triana, Trident and Pipeline Pilot workflows.
    • More group collaboration features
      • Group announcements
      • Group discussions
      • Group wiki pages
    • Ability to aggregate external blog content and associate it with your user profile
  • 40. Future – BioCatalogue
    • Fully curated catalogue of Web services
    • Building on the work carried out for myExperiment
    http://www.biocatalogue.org/
  • 41. Acknowledgements
  • 42. Come meet us at ISMB
    • Demo: Tues 22 nd July, 14:15
    • Stand: Booth 20, Manchester Bioinformatics
    For more information… http://www.myexperiment.org http://wiki.myexperiment.org http://rubyforge.org/projects/myexperiment/ Mailing list - [email_address] http://www.mygrid.org.uk http://www.biocatalogue.org Mailing list - [email_address]