MINI Electrophysiology and CARMEN

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A talk presented at the first MIBBI workshop on the CARMEN project and the MINI Electrophysiology document

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MINI Electrophysiology and CARMEN

  1. 1. Minimum Information about a Neuroscience Investigation MINI: Electrophysiology [email_address]
  2. 2. The CARMEN Project <ul><li>Enabling sharing and collaborative exploitation of data, analysis code and expertise that are not physically collocated </li></ul>
  3. 3. Consortium and Profile Stirling St. Andrews Newcastle York Sheffield Cambridge Imperial Plymouth Warwick Leicester Manchester
  4. 4. Virtual Laboratory Node Search for Data & Analysis Code Raw Signal Data Search & Visualisation Deployment of Data & Analysis Code in Processes Raw & Derived Data File Store Security Policies Controlling Access to Data & Code Structured Metadata Store Enabling Search & Annotation Analysis & Model Code Store Web based Interaction
  5. 5. MINI: Electrophysiology <ul><li>Subdivided as; </li></ul><ul><ul><li>Contact and context </li></ul></ul><ul><ul><li>Study subject </li></ul></ul><ul><ul><li>Recording location </li></ul></ul><ul><ul><li>Task </li></ul></ul><ul><ul><li>Stimulus </li></ul></ul><ul><ul><li>Behavioural event </li></ul></ul><ul><ul><li>Recording </li></ul></ul><ul><ul><li>Time series data </li></ul></ul>Study inputs Assay inputs Assay procedures Data
  6. 6. Implementation <ul><li>The content of each MINI document is structured via FuGE </li></ul><ul><ul><li>http://fuge.sourceforge.net/ </li></ul></ul><ul><li>Implemented via SyMBA – a database implementation of FuGE </li></ul><ul><ul><li>http://symba.sourceforge.net/ </li></ul></ul><ul><li>Develop associated ontologies and re-use where possible. e.g OBI </li></ul><ul><ul><li>http:// purl.obofoundry.org /obo/obi </li></ul></ul>
  7. 7. Benefits of MIBBI <ul><li>The ability to re-use existing checklists </li></ul><ul><li>More eyes, more robust guidelines </li></ul><ul><li>Consistent data representation with Neuroscience </li></ul><ul><li>Interoperability across life-science </li></ul><ul><li>Time re-directed to tools and applications and research </li></ul>
  8. 8. Acknowledgments <ul><li>The CARMEN consortium </li></ul><ul><li>Allyson Lister : SyMBA </li></ul>
  9. 9. References <ul><li>The CARMEN project </li></ul><ul><ul><li>www.carmen.org.uk </li></ul></ul><ul><li>MINI: Electrophysiology guidelines </li></ul><ul><ul><li>http://hdl.handle.net/10101/npre.2008.1720.1 </li></ul></ul><ul><li>FuGE </li></ul><ul><ul><li>http://fuge.sourceforge.net/ </li></ul></ul><ul><li>SyMBA </li></ul><ul><ul><li>http://symba.sourceforge.net/ </li></ul></ul>
  10. 10. License <ul><li>This document is licensed to the public under the Creative Commons Attribution 3.0 License </li></ul>

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