Source code used for the computational modeling and fitting presented in Figure 5 of Zenke et al, Immunity, 2020.
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
examples/run model with fits.ipynb
: example of running the model with fitted parametersexamples/fitting example.ipynb
: example of fitting algorithm
tcell_model_v7
: implementation of ODE modelfit_mc.py
: tools for running fits on multiple coresplotting_imports_nb.py
: plotting settings
expdata
: processed data from experimentsbest_fits
: best fits for flat, U-shaped and V-shaped wells for the model inrun model with fits.ipynb