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CARMEN is an e-Science Pilot Project aimed at developing a virtual laboratory for neurophysiology. It includes data collection, analysis, and collaboration tools for researchers in the field. Visit our website for more information.
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My Collaborators & Other Animals Alastair Knowles (Incognizant) Project Manager alastair.knowles@ncl.ac.uk
What is CARMEN? • e-Science Pilot Project (£4.5M October 2006) • 11 UK Universities to develop a virtual laboratory for neurophysiology • Development of core infrastructure at Newcastle and York • Partners from Plymouth to St. Andrews conducting neurophysiology
Neurophysiology – Data • The study of nervous system function • Primarily electrode recordings • Some imaging using magnetic and labelling techniques • Experiments in human and animal tissue • GBs/hour 10-25nm
Neurophysiology – Analysis • 64/128/256/512 ++ channels, 25,000 ++ samples/s • Spike detection and sorting • Identification of higher order correlations and patterns • Information theory • Network analysis • Models Signal Spikes
CARMEN – Team Architecture Developers Software Developers Metadata Project Manager Communication End User Experiments End User Models End User Analysis
Timescales • Release of data sharing infrastructure (imminent) • Release of analysis platform (Q1/Q2 2009)
Issues • Sharing • Metadata and annotation • Ownership and attribution • Community • Sustainability
Sharing • Like courtship • Small secretive groups with wide ranging territory • Difficult to find partners • Once found, don’t let somebody else find them! “Some partners were reluctant to describe/disclose collaborations with individuals external to the consortium. Further, a minority of partners were protective of their collaborations, e.g. reluctant to introduce collaborators including CARMEN partners to other prospective collaborators within the consortium.” – Alastair Knowles: Project Review Sept 2008.
Sharing • Are there any gold standard datasets that would encourage you to collaborate in CARMEN? “Partners were asked to specify third party resources (e.g. resources external to the project) that they would like to be made available to them in CARMEN. The majority identified resources belonging to their immediate collaborators external to CARMEN. A minority identified their own research as providing the most critical resources. There are no ‘gold standard’ resources.” – Alastair Knowles: Project Review September 2008. Collaborators Mine!
Metadata and Annotation: Genome • Triple helix (1953) • DNA Sequencing (1976-80) • Los Alamos sequence database (1979) • GenBank (1982)
Metadata and Annotation - Neurophysiology • Need to exchange lots of rich, freeform information • Cannot be constrained by structure • Need to find the needle in the haystack • Need to maintain individuality • Lingua franca: MINI (minimum information about a neurophysiology investigation) http://www.carmen.ncl.ac.uk/standards/mini.pdf
Ownership and Trust • Trust • Protracted ‘ownership’ • Just make everything open? • What species are you? Analysis Data 1 Data 2 Data 3
Community • Big picture? • Journals, funders?
Sustainability • Data sharing policy • Support for long term users • High cost solutions for niche audiences?
Preparing Exploring Reporting The Publisher The Newcomer The Explorer The Reporter The Consumer The Funder From Reporting To Preparing In the Ideal World ... Science Cloud
