myExperiment

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Accelerating Time to Experiment The
myExperiment Approach to Open Science
David De Roure Carole Goble Jiten Bhagat
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The social process of Science 2.0
Undergraduate Students
Digital Libraries
scientists
Graduate Students
experimentation
Data, Metadata Provenance WorkflowsOntologies
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• What is it?
• How we built it
• Towards the e-Laboratory

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• What is it?

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Trident
Taverna
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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 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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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
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myExperiment.org is
myExperiment Features

• User Profiles
• Groups
• Friends
• Sharing
• Tags
• Workflows
• Developer interface
• Credits and Attributions
• Fine control over privacy
• Packs
• Federation
• Enactment

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

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• How we built it

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For Developers
HTML
tags
reviews
ratings
profiles
groups
workflows
credits
friendships
packs
files
mySQL
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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

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Google Gadgets
Bringing myExperiment to the iGoogle user
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Taverna Plugin
Bringing myExperiment to the Taverna user
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Facebook
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Silverlight
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PREFIX rdf lthttp//www.w3.org/1999/02/22-rdf-synt
ax-nsgt PREFIX myexp lthttp//rdf.myexperiment.org
/ontologygt PREFIX sioc lthttp//rdfs.org/sioc/ns
gt select ?friend1 ?friend2 ?acceptedat where ?z
rdftype lthttp//rdf.myexperiment.org/ontologyFri
endshipgt . ?z myexphas-requester ?x . ?x
siocname ?friend1 . ?z myexphas-accepter ?y .
?y siocname ?friend2 . ?z myexpaccepted-at
?acceptedat
All accepted Friendships including accepted-at
time
Semantically-Interlinked Online Communities
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Six Principles of Software Design to Empower
Scientists

• Fit in, Dont 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

• Keep your Friends Close
• Embed
• Keep Sight of the Bigger Picture
• Favours will be in your Favour
• Know your users
• Expect and Anticipate Change

De Roure, D. and Goble, C. (2009) Six Principles
of Software Design to Empower Scientists. IEEE
Software (in press)
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• Towards the e-Laboratory

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

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• Contact
• David De Roure
• dder_at_ecs.soton.ac.uk
• Carole Goble
• carole.goble_at_manchester.ac.uk
• Thanks
• The myGrid Family, National Centre for e-Social
  Science, CombeChem, Scientific Workflow Community

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