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Update the growth module #104

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40 tasks done
GwennyGit opened this issue Oct 31, 2023 · 4 comments · Fixed by #119
Closed
40 tasks done

Update the growth module #104

GwennyGit opened this issue Oct 31, 2023 · 4 comments · Fixed by #119
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@cb-Hades @GwennyGit
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enhancement New feature or request refactoring changes in the code functionality
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New functions tow...

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@GwennyGit
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GwennyGit commented Oct 31, 2023 •
edited by cb-Hades
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The growth module works and contains excellent ideas. However, a new and less confusing setup would be beneficial. The following ideas should improve the setup and add better handling of flux values.

Improvement/rearranging of already existing functions (-> #79)

Main changes

  • Change existing functions:
    • Rename set_fluxes_to_simulate -> set_bounds_to_default
      • Change/add default parameter for upper & lower bound from COBRApy/user-specified
    • Merge get_default_uptake (renamed to get_model_uptake) & get_minimal_uptake -> Name function get_uptake
    • Replace get_missing_exchanges & modify_medium with medium.add_medium_to_model
    • Merge find_missing_essential & find_minimum_essential -> find_essential?
    • Further ideas for medium.add_medium_to_model -> ❗ name changed to medium_to_model:
      • Integrate functionality of find_essential ❓
      • Add a parameter to return the resulting medium
      • Add the possibility to load medium as anaerobic ❓
      • Extend usable namespaces from BiGG-specific to more namespaces
        • 🔴 this function can already do that, but not the wrappers in growth etc. -> see "still missing" below
    • Rename simulate_minimal_essential -> simulate_growth
      • Add parameter to enable growth with or without supplements
    • Merge growth_one_medium_from_default & growth_one_medium_from_minimal -> growth_on_one_medium
    • Check output of growth_on_one_medium & get_growth_selected_media
    • Remove get_growth_selected_media -> Now handled by medium.add_medium_to_model!
  • Check connections in/to:
  • Check pseudo algorithm

Additional ideas

  • Check model.optimize & model.slim_optimize -> Possibility for faster run time?
  • growth_on_one_medium:
  • Add possibility to add:
    • medium-specific fluxes from medium2substance table in data.db,
    • default flux (Currently: 10),
    • user-specific default flux and
    • user-specific fluxes -> 🟠 oxygen percentage can be set only currently
  • Improve handling of anaerobic simulations

Isolated functions

  • Change function get_default_secretion -> Wrong description for what it currently really does!
  • get_all_minimum_essential -> Do we need this? Is it correct? 🤔 -> Removed!
  • Rename get_essential_reactions -> get_single_ko_essential_reacs ❓
  • Rename get_essential_reactions_via_bounds -> get_single_deletion_essential_reacs ❓
  • Rename find_additives -> find_additives_to_enhance_growth/ find_growth_enhancing_additives ❓

Improvement/addition of new functions:

Still missing

  • function for reading external media: missing a 'file' option 🟠 written, only needs testing
  • adding superoxide to a medium to enable growth e.g. important for Klebsiella (either via subset or new category to add different substances) -> Update media definitions, document and extend db #16
@GwennyGit GwennyGit added enhancement New feature or request refactoring changes in the code functionality labels Oct 31, 2023
@cb-Hades cb-Hades mentioned this issue Nov 2, 2023
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Notes from the Whiteboard:

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get_default_secretion changed to one function for returning ID for reactions secreting compounds (get_secretion) and a second for for returning functions that produce a compound called get_production.

cb-Hades added a commit that referenced this issue Nov 21, 2023
@cb-Hades
Update growth simulation
9448f2b 
collected + started functions for growth simulation
added class for reports
#104
cb-Hades added a commit that referenced this issue Nov 21, 2023
@cb-Hades
Update growth.py
126372f 
restructering, renaming, some clean up #104
GwennyGit referenced this issue Nov 22, 2023
@cb-Hades
Update growth.py
d912c2d 
add/update set_bounds_to_default and get_uptake
GwennyGit referenced this issue Nov 22, 2023
@cb-Hades
re-initialise database
019600a
GwennyGit referenced this issue Nov 22, 2023
@cb-Hades
Further growth.py restructering
5fd6570
cb-Hades added a commit that referenced this issue Nov 29, 2023
@cb-Hades
Update growth.py
5331494 
Issue #104
- removed construction as functions have been moved to growth
- added function for parsing the media_config.yaml
- progress for growth_simulation function, next agenda: simulation & visualisation + testing
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
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cb-Hades commented Dec 5, 2023

Added functions to plot and save the growth simulation results.

cb-Hades added a commit that referenced this issue Dec 6, 2023
@cb-Hades
Changed Pseudocode to fit restructured module
c62e7e1 
#104
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.
cb-Hades added a commit that referenced this issue Dec 14, 2023
@cb-Hades
Fixing namespace option links #104
8a33c54
cb-Hades added a commit that referenced this issue Dec 19, 2023
@cb-Hades
Add substances + specific fluxes to medium
c0a0c69 
#104 , #99
- function to add a substance from db to medium
- changes to media_config to allow adding substances
- small docs additions
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
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All tasks are either done or transferred to a new issue -- closing issue (#16, #79).

@GwennyGit GwennyGit linked a pull request Apr 12, 2024 that will close this issue
Move changes from structure update to dev-2 #119
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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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Move changes from structure update to dev-2 draeger-lab/refinegems
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