accelerating time to experiment – the myexperiment approach to open science david de roure carole...
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Accelerating Time to Experiment –The myExperiment Approach to Open Science
David De Roure
Carole Goble
Jiten Bhagat
scientists
LocalWeb
Repositories
Graduate Students
Undergraduate Students
Virtual Learning Environment
Technical Reports
Reprints
Peer-Reviewed Journal &
Conference Papers
Preprints &
Metadata
Certified Experimental
Results & Analyses
experimentation
Data, Metadata Provenance WorkflowsOntologies
Digital Libraries
The social process of Science 2.0
• What is it?• How we built it• Towards the e-Laboratory
• What is it?
Kepler
Triana
BPEL
Ptolemy II
Taverna
Trident
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.
Reuse, Recycling, RepurposingReuse, Recycling, Repurposing
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.org is...myExperiment.org is...
myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs
myExperiment currently has 1331 registered users, 114 groups, 536 workflows, 147 files and 40 packs
myExperiment.org is…
User Profiles Groups Friends Sharing Tags Workflows Developer interface Credits and Attributions Fine control over privacy Packs Federation Enactment
myExperiment FeaturesmyExperiment Features
Ownership and AttributionOwnership and Attribution
The most important aspect of myExperimentDesigned by scientists
The most important aspect of myExperimentDesigned by scientists
PacksPacks
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
• How we built it
24/5/2007 | myExperiment | Slide 21
Search Engine
reviewsratingsgroupsfriendships
tags
Enactor
filesworkflows
`
HTML
For DevelopersFor Developers
RDF Store
SPAR
QL
endp
oint
Managed REST API
iGoogle
android
XML
APIconfig
mySQL
profiles
packscredits
For DevelopersFor 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
Google GadgetsGoogle Gadgets
Bringing myExperiment to the iGoogle userBringing myExperiment to the iGoogle user
Taverna PluginTaverna Plugin
Bringing myExperiment to the Taverna userBringing myExperiment to the Taverna user
FacebookFacebook
SilverlightSilverlight
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
1. Fit in, Don’t Force Change2. Jam today and more jam
tomorrow3. Just in Time and Just
Enough 4. Act Local, think Global 5. Enable Users to Add Value6. Design for Network Effects
1. Fit in, Don’t Force Change2. Jam today and more jam
tomorrow3. Just in Time and Just
Enough 4. Act Local, think Global 5. Enable Users to Add Value6. Design for Network Effects
Six Principles of Software Design to Empower ScientistsSix Principles of Software Design to Empower Scientists
1. Keep your Friends Close2. Embed3. Keep Sight of the Bigger
Picture4. Favours will be in your
Favour5. Know your users6. Expect and Anticipate
Change
1. Keep your Friends Close2. Embed3. Keep Sight of the Bigger
Picture4. Favours will be in your
Favour5. Know your users6. Expect and Anticipate
Change
De Roure, D. and Goble, C. (2009) Six Principles of Software Design to Empower Scientists. IEEE Software (in press)
• Towards the e-Laboratory
Workflow Monitoring
Event Logging
Social Metadata
Annotation Service
Search
User Registration
Distributed Data Query
Job Execution
Naming and Identity
Anonymisation
Text Mining
e-Lab Servicese-Lab Services
Research ObjectsResearch Objects
ReflectionsReflections
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
Contact
David De [email protected]
Carole [email protected]
Thanks
The myGrid Family, National Centre for e-Social Science, CombeChem, Scientific Workflow Community
