FuGE Update
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An update on the FuGE project and a database implementation called SyMBA presented at the first MIBBI workshop

An update on the FuGE project and a database implementation called SyMBA presented at the first MIBBI workshop

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FuGE Update FuGE Update Presentation Transcript

  • An update on the Functional Genomics Experiment (FuGE) model Frank Gibson 1 and Andy Jones 2 1 University of Newcastle and 2 University of Liverpool
  • License
    • This document is licensed to the public under the Creative Commons Attribution 3.0 License
  • FuGE model
    • Model of common components in science investigations, such as sample description, Experiment variables and design, data, protocols, equipment and software.
  • FuGE model
    • Three main uses:
      • Capture description / data for techniques that do not require a specific format
      • Additional metadata for existing data formats
      • Framework to be extended for creating new data formats
    • Aims:
      • bring about convergence of data formats across the omics
      • develop open-source toolkits for simplifying the integration of data and submission to public repositories
  • FuGE Availability
    • http://fuge.sourceforge.net/
    • FuGE version 1 released Aug 2007
    • First version of toolkit released in Jan 2008
    • Jones et al. Nature Biotech 25, 1127 - 1133 (2007) PMID: 17921998
  • FuGE Implementation - Extension
    • Can be extended to cover the specifics of a particular experiment
    • Dec 2007 - workshop bringing together groups developing extensions on FuGE:
      • proteomics (GelML, spML, analysisXML),
      • flow cytometry,
      • RNAi,
      • e-Neuroscience
    • Also being used in various ways for modelling microarray data, metabolomics, genetical genomics, immunohistochemistry...
  • Tools and software
    • Tooling
      • Toolkit now available for generating XML Schema from model
      • Toolkits for generating database back-end and XML input/output released in beta versions
    • Software implementations
      • On-going projects to develop converters between FuGE-ML and tab formats (EBI), generic XML data input and dissemination (Manchester)
      • Symba (Newcastle), SystemX (Basel), CPAS (Fred Hutch), Genologics
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  • Getting involved...
    • See the FuGE website http:// fuge.sourceforge.net /
    • Read the documentation:
      • FuGE version 1 ( http://fuge.sf.net/dev/V1Final/FuGE-v1-SpecDoc.doc )
      • Nature Biotech paper ( http://www.nature.com/nbt/journal/v25/n10/full/nbt1347.html )
      • Workshop report (coming soon)
      • Toolkit documentation ( http://fuge.sourceforge.net/stks/xsd-stk/index.html )
    • Contact FuGE mailing list: fuge-devel@lists.sourceforge.net#
    • Look at an implementation Symba: http://symba.sourceforge.net/