About different applications

As refineGEMs includes a number of different functionalities, this page lists some of the possible applications of refineGEMs in the context of different areas of model curation.

Model refinement

• Automated polishing
• Biomass normalisation
• Energy generating cycles (EGCs)
  • Identify EGCs
  • Solve EGCs
    • Greedy approach
• Gap-filling
  • (Semi-)automated gap-filling algorithms
    • Gap-filling with KEGG
    • Gap-filling with BioCyc
      • Data acquisition from BioCyc
    • Gap-filling with a GFF (and SwissProt)
  • How to run a GapFiller

Model annotation

• Pathway addition
  • Add KEGG pathways from reaction:
• SBO-Term annotation

Analysis and simulation

• Growth simulation
  • Growth
  • Auxothrophy
  • Source test
  • Minimal medium
• Statistical report
  • How to create the ModelInfoReport
    • via command line
    • inside Python
  • Examplary ModelInfoReport visualisation

Further examples

• Application examples
  • Loading a model