VisANT

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)