Jiten Bhagat

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myExperiment social software for sharing
workflows
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
BOSC 2008
www.myexperiment.org
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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.

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Use myExperiment to
Build packs of related content
Find people and make friends
Share your workflows and files
Create and join groups of similar interests
Control access to your workflows and files
Build your profile and reputation
Find workflows and files that others have shared
Have discussions and collaborate
Execute workflows directly within myExperiment
(if you have access to a remote Taverna enactor)
Maintain and use different versions of workflows
Tag and rate workflows and files
Write reviews and comments
Send messages to other people on myExperiment
Reuse and repurpose workflows (and other files!)
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Bare Facts
Mar 2007 start of project Jul 2007 closed
beta Nov 2007 open beta

• 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

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Vitals July 2008
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

• 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)

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Setting the context

• Why do we need an environment like myExperiment?

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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
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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

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Taverna
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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.

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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.

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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 Pauls 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.

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As Tavernas 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.
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myExperiment enables scientists to discover,
reuse and repurpose workflows, and to enact them
from a web page using a remote enactment service.
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Workflow Components

• See the internals of a workflow
• Aids decision making when deciding on
  reuse/repurposing

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Workflow Enactment
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myExperiment focuses on the special requirements
of scientists, providing support for ownership,
credit and attribution, licensing, visibility
and sharing.
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Workflow Upload
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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

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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.
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Workflows have friends (and social metadata) too!

• Emphasising social networking around the
  workflows.
• Attributions show what workflows/files its based
  on ( reuse/repurpose).

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myExperiment is not just about workflows, its
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.
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Packs
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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.
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Google Gadgets
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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.

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myExperiment is an open source codebase (released
under the BSD licence). Individuals and
laboratories are free to install their own
myExperiment instances.
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Developer Support

• Anyone can download and set up their own
  myExperiment - http//rubyforge.org/projects/myexp
  eriment/
• We have a new wiki to support external developers
  and their projects http//wiki.myexperiment.org/
  

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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

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Future BioCatalogue

• Fully curated catalogue of Web services
• Building on the work carried out for myExperiment

http//www.biocatalogue.org/
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Acknowledgements
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Come meet us at ISMB

• Demo Tues 22nd July, 1415
• Stand Booth 20, Manchester Bioinformatics

• For more information
• http//www.myexperiment.org
• http//wiki.myexperiment.org
• http//rubyforge.org/projects/myexperiment/
• Mailing list - myexperiment-discuss_at_nongnu.org
• http//www.mygrid.org.uk
• http//www.biocatalogue.org
• Mailing list - biocatalogue-friends_at_listserv.manch
  ester.ac.uk