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Enhance growth simulation #79

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2 of 7 tasks
GwennyGit opened this issue Apr 19, 2023 · 0 comments
Open
2 of 7 tasks

Enhance growth simulation #79

GwennyGit opened this issue Apr 19, 2023 · 0 comments
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enhancement New feature or request refactoring changes in the code functionality

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@GwennyGit
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GwennyGit commented Apr 19, 2023

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
  • test connection to main.py

Further ides

  • implement source test, e.g. for C, N, S, ...
  • Allow user-specified supplementation
  • Crop heatmaps according to no growth in growth report
@GwennyGit GwennyGit added enhancement New feature or request refactoring changes in the code functionality labels Apr 19, 2023
@GwennyGit GwennyGit mentioned this issue Oct 31, 2023
40 tasks
cb-Hades added a commit that referenced this issue Dec 4, 2023
#104 , #79
Update growth simulation + plotting model vs media (bars and heatmap)
cb-Hades added a commit that referenced this issue Dec 5, 2023
small fixes and added docstrings
#104 , #79
cb-Hades added a commit that referenced this issue Dec 5, 2023
added a function to save the report as a whole
#104
#79
cb-Hades added a commit that referenced this issue Dec 6, 2023
Still needs testing as a whole.
#104 , #79
GwennyGit added a commit that referenced this issue Dec 7, 2023
- Added functionality to not only add a new medium but also an updated version. -> Needs to be tested!
- Added function to generate a new SQL file after updating the database. -> Works but looks less human-readable compared to the current SQL file.
cb-Hades added a commit that referenced this issue Feb 7, 2024
- completed corresponding report class with save and visualisation functions
- fixed problem with 'BiGG+VMH' label in export_to_model in medium.py
cb-Hades added a commit that referenced this issue Feb 7, 2024
cb-Hades added a commit that referenced this issue Feb 12, 2024
cb-Hades added a commit that referenced this issue Feb 14, 2024
cb-Hades added a commit that referenced this issue Feb 14, 2024
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Labels
enhancement New feature or request refactoring changes in the code functionality
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