Paper Plan

  1. PV2 - case study, real data (Martijn) May-July
  2. PPPiP (Andra) May-July
  3. Gene database system (Martijn/Alex) June-Aug
  4. Metabolomics and pathway analysis (Martijn/Thomas) Aug-Oct
  5. GenMAPP-CS (Alex) Sept-Nov
  6. Pathway analysis revisited: current state, new information and tools, future (Thomas/Alex) Oct-Dec
  7. WikiPathways community and general report (Thomas/Alex/Martijn)2010
  8. PV and GPML libs as toolkit (Martijn/Thomas) 2010

BridgeDB Database System

  • Derby pgdbs
  • MySQL server
  • Web service: RESTful queries
  • Primary and alternative sources for PathVisio/WikiPathways and GenMAPP-CS
    • ID unification and mapping
    • backpages
    • linkouts
    • annotation of nodes
  • Generic source for bioinformatics tools

Analysis tools

  • PV2
  • GO Elite
  • GenMAPP-CS

WikiPathways Projects

  • Custom installations
    • WikiPathways-Cell - for cell type-specific collections of pathways