/Tcellactivation_ODE_Immunity2020

Code needed for the modeling and fitting in Zenke et al, Immunity, 2020

Primary LanguageJupyter NotebookMIT LicenseMIT

Source code used for the computational modeling and fitting presented in Figure 5 of Zenke et al, Immunity, 2020.

Set up python

The notebooks (.ipynb) run in jupyterlab or jupyter notebook, for this you'll need to install jupyter.

When you have a jupyter environment, either install the required packages:

  • using pip: pip install numpy scipy matplotlib seaborn pandas statsmodels pyDOE prettytable
  • using conda: conda install numpy scipy matplotlib seaborn pandas statsmodels pyDOE prettytable

Contents

Notebooks

  • examples/run model with fits.ipynb: example of running the model with fitted parameters
  • examples/fitting example.ipynb: example of fitting algorithm

Source files

  • tcell_model_v7: implementation of ODE model
  • fit_mc.py: tools for running fits on multiple cores
  • plotting_imports_nb.py: plotting settings

Data files

  • expdata: processed data from experiments
  • best_fits: best fits for flat, U-shaped and V-shaped wells for the model in run model with fits.ipynb