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draeger-lab / refinegems

refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
https://refinegems.readthedocs.io/en/latest/
MIT License
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Enhance growth simulation #79

Open GwennyGit opened 1 year ago

GwennyGit commented 1 year ago

Current functionalities of the growth module

  1. simulate growth (one model & multiple models)
  2. based on configuration file or direct input
  3. supplement media to enable growth e.g. based on minimal medium as calculated by COBRApy
  4. find growth enhancing exchanges
  5. auxotrophy simulation (proteinogenic amino acids)
  6. find minimal medium based on different conditions

    Under construction

    • [ ] more namespace options in addition to BiGG IDs
    • [ ] MetaNetX
    • [ ] SEED
    • [x] test connection to main.py

      Further ides

    • [x] implement source test, e.g. for C, N, S, ...
    • [ ] Allow user-specified supplementation
    • [ ] Crop heatmaps according to no growth in growth report