VisANT

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Revision as of 19:46, 15 May 2009 by Tgibbons (talk | contribs)
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This is just a summary of my notes on VisANT from reading the user manual[1]

Useful Features

  • Integration with KEGG plus several other online databases/tools
  • Accessibility
    • Web based utility
    • Downloadable for local jobs
    • Hybrid version can save data to local machine while running on BU machines
  • Shortest path calculation
    • Sensitive to directionality
  • Metanodes
    • Allow for cleaner visualization of large, complex pathways and multi-protein enzyme complexes
    • Allow for multiple instances of proteins/compounds
  • Plug in support
  • Filter based on methods
    • Add new method (eg. "Metagenomic Analysis")
    • Unselect all methods then reselect "Metagenomic Analysis" to view only those nodes and edges revealed by metagenomic analysis
  • Batch mode for large-scale applications

Missing Features

  • Mapping sequence data to genes
    • Distributed BHR calculation
  • Non-metabolic pathways
    • KEGG has yet to release KGML files for the following pathways:
      • Genetic information processing
      • Environmental information processing
      • Cellular processes
      • Human diseases
      • Drug development
  • Open source?
    • "Partially funded by NIH" (probably means they're required to release source)