We used biomass==0.5.2 for mathematical modeling.
The package can be installed via pip:
$ pip install biomass==0.5.2
This requires Python 3.7 or later.
We generated two mathematical models, TGFb_model/ and TGFb_VEGF_model/, in this study. Each related files can be found under each model directory.
| Name | Content |
|---|---|
[MethodS.md] |
Differential equation, parameters and initial condition |
[name2idx/] |
Names of model parameters and species |
[out/] |
Parameter values that are estimated from experimental data |
[reaction_network.py] |
Reaction indices grouped according to biological processes |
[set_model.py] |
Differential equation, parameters and initial condition to run biomass |
[observalbe.py] |
Observables, simulations and experimental data |
[viz.py] |
Plotting parameters for customizing figure properties |
[set_search_param.py] |
Lower and upper bounds of model parameters to be estimated |
[fitness.py] |
An objective function to be minimized, i.e., the distance between model simulation and experimental data |
[optimize.py] |
Run to estimate parameter values from experimental data |
[simulate.py] |
Run for simulation, visualization of estimated parameter sets and objective function trajectories, and sensitivity analysis |