Analysis of Context Specific Metabolic Models

This notebook can be downloaded from this link

Define model_names with their associated paths in a dict

model_paths = {
    "epithelial_csm": "epithelial_csm.xml",
    "mesenchymal_csm": "mesenchymal_csm.xml"
}

Import analysis module from gsmm

analyse_and_save_fluxes(..) is a function that carries all the analysis and saves the data for further analysis to be utilised by visualisation module

from gsmm.csm.analyse_csm import analyse_and_save_fluxes

analyse_and_save_fluxes(model_paths)

2024-07-10 01:15:54,415 - INFO - The current solver interface glpk doesn't support setting the optimality tolerance.

Loading model: epithelial_csm from epithelial_csm.xml...

2024-07-10 01:15:54,857 - INFO - Loaded model: epithelial_csm from epithelial_csm.xml
2024-07-10 01:15:55,806 - INFO - The current solver interface glpk doesn't support setting the optimality tolerance.

Successfully loaded model: epithelial_csm
Loading model: mesenchymal_csm from mesenchymal_csm.xml...

2024-07-10 01:15:56,280 - INFO - Loaded model: mesenchymal_csm from mesenchymal_csm.xml
/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/gsmm/csm/analyse_csm.py:130: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.


  df['Flux'].fillna(0, inplace=True)
2024-07-10 01:15:56,599 - WARNING - Metabolite damp_c not found in model epithelial_csm
2024-07-10 01:15:56,608 - WARNING - Metabolite mag__hs_c not found in model epithelial_csm
2024-07-10 01:15:56,609 - WARNING - Metabolite lpchol_hs_c not found in model epithelial_csm
2024-07-10 01:15:56,609 - WARNING - Metabolite hdcea_c not found in model epithelial_csm
2024-07-10 01:15:56,609 - WARNING - Metabolite hdca_c not found in model epithelial_csm
2024-07-10 01:15:56,609 - WARNING - Metabolite ocdcea_c not found in model epithelial_csm
2024-07-10 01:15:56,610 - WARNING - Metabolite ocdca_c not found in model epithelial_csm
2024-07-10 01:15:56,610 - WARNING - Metabolite ptrc_c not found in model epithelial_csm
2024-07-10 01:15:56,611 - WARNING - Metabolite spmd_c not found in model epithelial_csm
2024-07-10 01:15:56,611 - WARNING - Metabolite sprm_c not found in model epithelial_csm
2024-07-10 01:15:56,619 - WARNING - Metabolite Q10_c not found in model epithelial_csm
2024-07-10 01:15:56,619 - WARNING - Metabolite paps_c not found in model epithelial_csm

Successfully loaded model: mesenchymal_csm
Extracting fluxes for model: epithelial_csm...
Optimizing model: Recon3D...
Optimization completed for model: Recon3D
Extracting fluxes for model: mesenchymal_csm...
Optimizing model: Recon3D...
Optimization completed for model: Recon3D
Flux extraction complete.
Filtering fluxes with threshold: 1...
Filtering complete. Number of reactions above threshold: 271
Collecting sink fluxes for model: epithelial_csm...
Warning: Metabolite damp_c not found in model epithelial_csm
Warning: Metabolite mag__hs_c not found in model epithelial_csm
Warning: Metabolite lpchol_hs_c not found in model epithelial_csm
Warning: Metabolite hdcea_c not found in model epithelial_csm
Warning: Metabolite hdca_c not found in model epithelial_csm
Warning: Metabolite ocdcea_c not found in model epithelial_csm
Warning: Metabolite ocdca_c not found in model epithelial_csm
Warning: Metabolite ptrc_c not found in model epithelial_csm
Warning: Metabolite spmd_c not found in model epithelial_csm
Warning: Metabolite sprm_c not found in model epithelial_csm
Warning: Metabolite Q10_c not found in model epithelial_csm
Warning: Metabolite paps_c not found in model epithelial_csm
Extracted sink fluxes for model: epithelial_csm
Collecting sink fluxes for model: mesenchymal_csm...

2024-07-10 01:15:56,760 - WARNING - Metabolite damp_c not found in model mesenchymal_csm
2024-07-10 01:15:56,768 - WARNING - Metabolite mag__hs_c not found in model mesenchymal_csm
2024-07-10 01:15:56,768 - WARNING - Metabolite lpchol_hs_c not found in model mesenchymal_csm
2024-07-10 01:15:56,768 - WARNING - Metabolite hdcea_c not found in model mesenchymal_csm
2024-07-10 01:15:56,776 - WARNING - Metabolite ocdcea_c not found in model mesenchymal_csm
2024-07-10 01:15:56,777 - WARNING - Metabolite ocdca_c not found in model mesenchymal_csm
2024-07-10 01:15:56,777 - WARNING - Metabolite spmd_c not found in model mesenchymal_csm
2024-07-10 01:15:56,777 - WARNING - Metabolite sprm_c not found in model mesenchymal_csm
2024-07-10 01:15:56,778 - WARNING - Metabolite Q10_c not found in model mesenchymal_csm
2024-07-10 01:15:56,778 - WARNING - Metabolite paps_c not found in model mesenchymal_csm
2024-07-10 01:15:56,782 - INFO - Data saved to flux_data.pkl and sink_flux_data.pkl

Warning: Metabolite damp_c not found in model mesenchymal_csm
Warning: Metabolite mag__hs_c not found in model mesenchymal_csm
Warning: Metabolite lpchol_hs_c not found in model mesenchymal_csm
Warning: Metabolite hdcea_c not found in model mesenchymal_csm
Warning: Metabolite ocdcea_c not found in model mesenchymal_csm
Warning: Metabolite ocdca_c not found in model mesenchymal_csm
Warning: Metabolite spmd_c not found in model mesenchymal_csm
Warning: Metabolite sprm_c not found in model mesenchymal_csm
Warning: Metabolite Q10_c not found in model mesenchymal_csm
Warning: Metabolite paps_c not found in model mesenchymal_csm
Extracted sink fluxes for model: mesenchymal_csm
Sink flux collection complete.
Saving data to flux_data.pkl...
Data saved successfully to flux_data.pkl and sink_flux_data.pkl

from gsmm.csm.visualisation import plot_fluxes