Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Enhance growth simulation #79

Open
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
Assignees
@cb-Hades @GwennyGit
Labels
enhancement New feature or request refactoring changes in the code functionality
Milestone
New functions tow...

Comments

@GwennyGit
Copy link
Collaborator

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

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
Closed
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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@cb-Hades cb-Hades

@GwennyGit GwennyGit

Labels
enhancement New feature or request refactoring changes in the code functionality
Projects
None yet
Milestone
New functions towards future versions
Development

No branches or pull requests
2 participants
@cb-Hades @GwennyGit