collaboration and sharing
DESCRIPTION
Presented by Carole Goble at the JISC Future of Research Conference, 19th October 2010TRANSCRIPT
Collaboration and sharing computational research methods
Carole GobleUniversity of Manchester, [email protected]
Scientific research is generally held to be of good provenance when it is documented in detail sufficient to allow reproducibility.
http://en.wikipedia.org/wiki/Provenance#Science
Materials +
Methods+
Results=
Publication
In silico Experimental Standard Operating, Procedures, Protocols, Plans
http://usefulchem.wikispaces.com/page/code/EXPLAN001
E. Science laboris: in silico experimentsAutomated, reusable scripted analysis pipelines - workflows
Data processing , data chainingData and tool integrationAnnotation pipelinesAnalyticsSimulation steering and parameter sweepsPublication miningModel and hypothesis buildingResult Validation and comparisonData cleaning, curation and preservation
Shield from clouds and clusters details.Record provenance: steps, methods, results
http://www.mygrid.org.uk/tools/taverna/
Genetic variation in cattle species. Food security, biodiversity.
Resistance to African trypanosomiasis infection (sleeping sickness)
Liverpool (Kemp), Manchester (Brass), Nairobi
Comparing new data with reference genomes, prior results and the literature to identifying interesting differences
22 million SNPs
Little Science + Big Science
http://www.genomics.liv.ac.uk/tryps/trypsindex.html
Bottom up Effectiveness in Research
• Automated, repeatable, tracked plumbing– Using institutional and community computing
infrastructures, tools and datasets• Easier access to best of breed and “surfing” results
– non-developers access to sophisticated codes and applications, shielded from nasty computing details.
• Leverage applications, services, datasets and codes shielded from computing details. – Honors original codes and applications. Heterogeneous
coding styles and tools sets. The best applications.• Extensibility, adaptability & innovation.
– My stuff. Variant design.
Reuse, Recycle, Repurpose, Mash, Trade, Publish
Dr Paul Fisher
Dr Jo Pennock
Identify biological pathways implicated in resistance to Trypanosomiasis in cattle using mouse as a model organism.
Identify the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the whipworm parasite.
Levison S.E., et al Inflammatory Bowel Diseases (2010)
Fisher P, et al Nucleic Acids Research, 2007, 35(16) 5625-5633
Global Long Tail
How do I find and share methods across the
institution, communities, the web ?
How do I connect with other authors and users?
How do I know if its any good or right for me?
Who else is using it?
Where do I comment on my experiences?
http://www.myexperiment.org
• Socially share, discover, review and reuse workflows and other scientific methods.
• Cooperative market place.• A scientific gateway.
• Commons-based Production + Social networking
• Primary contribution, reviewing and curating.
Find experts and peers, advice, workflows, packs
Contribute, review and curate workflows
Train and educateLaunch workflows Cloud Methods Commons
http://www.myexperiment.org
Facts and Figures: Boutique but Beautiful
• Public Service: 1325 workflows, 349 files, 138 packs, 4129 registered members, 235 groups, 56 different countries, ~ 3000 unique hits per month. Workflows viewed/downloaded many 1000s of times.
• Adopted by 19 workflow systems and integrated into workflow workbenches: Galaxy, Taverna– Biology, chemistry, image analysis, social science, astronomy, engineering,
music…– Specialised clones in Music & NeuroScience. – Focus of research on workflow patterns and analytics.
• JISC funding since 2007• (Other funding: Microsoft, EU, EPSRC, BBSRC)
Effectiveness and Open CollaborationOpen platform, off the shelf components, open development, open linked data, Web 3.0 funky
Google gadgets
Application plugins
Linked Data Cloud
Friends, colleagues, resources
Literature
Images
LogBook
SoftwarePresentations
Data (files, spreadsheets)
Compute resources
Backup and Archive
WorkbenchGadgets
Publishing
[Duncan Hull]
Social collaboration environments (“e-Laboratories”) Collaboration, acceleration and transparency through Human Computation
Workflow management system Collaboration, acceleration and transparency through Automated Computation.
http://www.mygrid.org.uk
Institutional challenges
Adoption of Reproducible MethodsNew Publishing and Learning Objects
Pre-and Post Publication Metadata DifferentialsCitation, Credit and Reputation
Curation Costs
Methods Matter
Reproducible (or at least
defendable) Research
many eyes
Science 2010
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
[De Roure]
Actionable scholarly publishing & learning
Actionable Compound Research Objects
Data and Method burialSupplementary informationText miningThe rise of the Wiki
Competitive advantage.Adoption.
Credit.Help.Fame.
Reputation.
Being scooped.Scrutiny.
Misinterpretation.Cost.
Blame. Reputation.
Rew
ards
Risk
s
Nature 461, 145 (10 September 2009)
Trust
“Its not ready yet”
“I need to get (another) publication first”
“We don’t have the resources or skills to prepare it for others, esp. now we finished that project”
“Its faster/easier to do it myself, and will get the credit/control too”
“Its not described enough to be usable”
“I don’t trust the quality. Its not reliable enough. Its too noisy.
“Others won’t use it properly.” “Its not worth my while”
Sharing Governance ….
Credit & Reputation Quality & ReassuranceProvenance
Crowd Contribution
CreditRewardCareerUse ProfilesCitation
Method Building too.
Nature 2008
Credit and Reputation
T Shirts are not enough
Software
Community building
Automation
Social & Cultural
Coordination
GovernanceQUALITY for REUSE
Sustainability
Public Service
Community generated and curated Content
Open Software
Teaching aid
Methodology
Dig Library/Repository
Social network
Computer science researchSoftware engineeringComputational researchersResearchersSocial Science Social experiment
Collaboration platform
Free like puppies
Take Home: Methods Matter.
• Workflows are a transformative mechanism of connecting tools and encoding know-how– Scientists stand on the shoulders of resource experts
• myExperiment is a example of a collaborative environment for connecting workflow authors and users– Authors stand on the shoulders of each other
• The Power of Collectivism.• Rewards and risks of researchers in competitive
research.• Cultural shift in reward, adoption and support for
building, sharing and curating computational methods.
AcknowledgementsmyExperiment Director: David De Roure
Developers• Jiten Bhagat• Don Cruickshank• Danius Michaelides • David Newman• Sergejs Aleksejevs• Mark Borkum• Matt Lee• Tom Foster
Allied, Contributing Projects• Thomas Laurent• Eric Nzuobontane • Ian Dunlop• Stuart Owen• Shoaib Sufi• Sean Bechhofer• Rodrigo Lopez• Steve Pettifer• Mannie Tags• Finn Bacall• Sarah Thew• Matt Gamble• Tim Clark
Users• Katy Wolstencroft• Paul Fisher• Duncan Hull• Franck Tanoh• Andrea Wiggins• Marco Roos• Jerzy Orlowski• Olga Krebs• Wolfgang Mueller• Tony Linde
Social Scientists• Yuiwei Lin• Rob Proctor• Meik Poschen• Jonathan Foster
Sponsors• Savas Parastatidis • Roger Barga• Derick Campbell• Tony Hey
