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
  • Enhancing the gene product annotations
• 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
      • Required BioCyc input files
      • How to get the tables from BioCyc
    • Gap-filling with a GFF (and a DIAMOND database)
      • Required GeneGapFiller input files
  • How to run a GapFiller
• Reaction direction
  • How to get the table from BioCyc

Model annotation

• Annotation polishing
  • When to use
• Pathway addition
  • Add KEGG pathways from reactions:
• SBO-Term annotation

Analysis and simulation

• Model comparison
  • Pan-core model construction
  • Comparing a model to a pan-core model
  • Comparing SBO annotations
• Growth simulation
  • Growth
  • Auxothrophy
  • Source test
  • Minimal medium
• Statistical report
  • How to create the ModelInfoReport
    • Via command line
    • Inside Python
  • Examplary ModelInfoReport visualisation

Media

• Media export
  • Export all media
  • Export selected media
  • Export from a media configuration file
  • Export formats
  • Example output