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An Overview of Intersect’s GDM System

An Overview of Intersect’s GDM System. Joe Thurbon Intersect. Prelude. The Brief. The research activities and communities it supports  The data management and analysis issues it seeks to resolve The types and volumes of data/metadata it will manage 

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An Overview of Intersect’s GDM System

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  1. An Overview of Intersect’sGDM System Joe Thurbon Intersect

  2. Prelude

  3. The Brief • The research activities and communities it supports  • The data management and analysis issues it seeks to resolve • The types and volumes of data/metadata it will manage  • The philosophy behind its design (e.g. why use semantic web technologies, if you are)

  4. Supported Communities

  5. Issues Addressed

  6. Issues Addressed

  7. Data / Metadata • We keep • All the short reads • All the bioanalyser output • All the trimmed reads • All the tertiary analysis output ‘that works’ • All parameters used to generate all of the above • Chemistry versions • Command line parameters • Species, Locations, etc

  8. Data Counts Data Sizes

  9. Philosophy • Anthropology • Epistemology • History and Philosophy of Science • Bio-informatics • GDM

  10. What do people do?

  11. What to Researchers do?

  12. What do Scientists do?

  13. What do Bio-Informaticians do?

  14. What does GDM Do? • Allows bio-informaticians to • Stand on the shoulders of giants (including themselves) • Record their observations • Record their experimental parameters • Manage their data • Iteratively

  15. Demo Metadata + Data + Parents = One Results • A results corresponds to a single experiment • What experiment did I do? (steps) • What parameters did I set? (parameters) • What observations did I make? (outputs) • When did I end up with (data) • What did I start from? (parents)

  16. SCU Ramaciotti VELVET Tcoffeee VELVET BLAST GDM Repository ANU AC3 VELVET EMBL DDBJ NCBI BLAST BLAST

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