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

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