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Enhance growth simulation #79

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2 of 6 tasks
GwennyGit opened this issue Apr 19, 2023 · 0 comments
Open
2 of 6 tasks

Enhance growth simulation #79

GwennyGit opened this issue Apr 19, 2023 · 0 comments
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@cb-Hades @GwennyGit
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enhancement New feature or request refactoring changes in the code functionality
Milestone
New functions tow...

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@GwennyGit
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GwennyGit commented Apr 19, 2023 •
edited by cb-Hades

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
@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
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40 tasks
GwennyGit referenced this issue Oct 31, 2023
@GwennyGit
Added source and flux for medium 'Blood' #49
77dd0d2
cb-Hades added a commit that referenced this issue Dec 4, 2023
@cb-Hades
Update growth_simulation
231e232 
#104 , #79
Update growth simulation + plotting model vs media (bars and heatmap)
cb-Hades added a commit that referenced this issue Dec 5, 2023
@cb-Hades
Update reports.py
b6b28f1 
small fixes and added docstrings
#104 , #79
cb-Hades added a commit that referenced this issue Dec 5, 2023
@cb-Hades
Update reports.py
49a96e9 
added a function to save the report as a whole
#104
#79
cb-Hades added a commit that referenced this issue Dec 6, 2023
@cb-Hades
Added 'file' option to read_external_medium
295eebc 
Still needs testing as a whole.
#104 , #79
GwennyGit added a commit that referenced this issue Dec 7, 2023
@GwennyGit
[Not tested yet!] Updated medium.py #79 #104
b05df9e 
- 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.
GwennyGit added a commit that referenced this issue Dec 20, 2023
@GwennyGit
Reverted update-media-in-db-related changes in medium.py #16 #79 #104
2cc355e
cb-Hades added a commit that referenced this issue Feb 7, 2024
@cb-Hades
Added source test to growth #79
0350363 
- 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 docs for source test #79
8bdf04c
cb-Hades added a commit that referenced this issue Feb 12, 2024
@cb-Hades
Small update growth.py #79
f54a7e6
cb-Hades added a commit that referenced this issue Feb 14, 2024
@cb-Hades
hotfix growth #79
607a348
cb-Hades added a commit that referenced this issue Feb 14, 2024
@cb-Hades
Hotfix 3 #79
342399d
GwennyGit added a commit that referenced this issue Feb 19, 2024
@GwennyGit
Adjusted retrieval of media list in save_user_input #79
390d0cf
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@GwennyGit GwennyGit

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enhancement New feature or request refactoring changes in the code functionality
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New functions towards future versions
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