François Bertaux

quantitative biology


Here are listed some pieces of code I wrote in the course of my research, including some code used in published papers. They are often in a quite raw form, but I would be really happy to clean / improve / clarify if someone asks me to !


A small python code providing useful analytical functions and parameterization algorithms for a popular stochastic gene expression model.

Existing as a github repository.


Code used for simulating TRAIL-induced apoptosis in this PLoS Comp Bio 2014 paper. The model accounts for stochastic gene expression together with protein-level apoptosis signaling and is not simply an ODE model or a fully stochastic model: it's hybrid, hence the h in hEARM (EARM is the name of the original TRAIL-induced apoptosis models developped in the lab of Peter Sorger at Harvard Medical School).

Existing as a github repository.


A tool to generalize the modeling approach with used for TRAIL-induced apoptosis (see hEARM) to other signal transduction pathways. The user defines the pathway reactions in python and c++ simulation code is generated.

To appear as a github repository very soon.


A tool describe multi-scale models of cell population dynamics (in python) and generate c++ code allowing their simulation. Currently no spatial capabilities (but can be used for liquid population dynamics simulations).

To appear as a github repository very soon.

Contact: Email. Also on ResearchGate, LinkedIn, twitter.