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An Overview of Intersect’s GDM System

Explore Intersect’s GDM system, supporting a range of research activities and communities, addressing data management and analysis issues, managing diverse data/metadata types and volumes, incorporating a philosophy focused on semantic web technologies. Learn about the supported communities and the core issues addressed.

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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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