2018_Heldt_et_al

Custom code for the article:
"A comprehensive model for the proliferation-quiescence decision in response to endogenous DNA damage in human cells"
Frank S. Heldt, Alexis R. Barr, Sam Cooper, Chris Bakal, Bela Novak
PNAS, February 2018, doi: 10.1073/pnas.1715345115

This repository contains different versions of the mathematical model used in the article.

• HeldtBarr2018_QuiescenceInResponseToDnaDamage_SBtoolbox: Deterministic version of the model for the Systems Biology Toolbox 2 (now known as IQR Tools, https://iqrtools.intiquan.com/) for MatLab. This file was used to obtain most of the deterministic simulations in the manuscript and served as a basis for the stochastic implementation.
• HeldtBarr2018_QuiescenceInResponseToDnaDamage_XPP: Deterministic version of the model for XPP-Aut (http://www.math.pitt.edu/~bard/xpp/xpp.html). Modified versions of this file were used to create bifurcation diagrams.
• HeldtBarr2018_QuiescenceInResponseToDnaDamage_SBML: Deterministic version of the model in the Systems Biology Markup Language (http://sbml.org), level 3 version 1. This file was created from the Copasi version of the model to provide compatibility with other software tools.
• HeldtBarr2018_QuiescenceInResponseToDnaDamage_Copasi_Deterministic: Deterministic version of the model for Copasi (http://copasi.org/). Simulating this file will recreate Fig. 1B.
• HeldtBarr2018_QuiescenceInResponseToDnaDamage_Copasi_Stochastic: Stochastic version of the model for Copasi (http://copasi.org/). Simulating this file provides a single stochastic realisation of the model similar to Fig. 1F and G. Stochastic simulations in the article were, however, created with a custom-made MatLab implementation of the Stochastic Simulation Algorithm not provided here.