2017_Barr_et_al

Custom code for the article:
"DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression"
Alexis R. Barr, Samuel Cooper, Frank S. Heldt, Francesca Butera, Henriette Stoy, Jörg Mansfeld, Bela Novak, Chris Bakal
Nature Communications, March 2017, 8:14728, doi: 10.1038/ncomms14728, http://www.nature.com/articles/ncomms14728

This repository contains two folders providing custom-made Matlab scripts for cell tracking and feature extraction ('Cell Tracking'), and different versions of the mathematical model used in the article ('Mathematical Modelling').

Cell Tracking

This folder contains the set of scripts and code used for tracking. Whilst we make the code available, due to the size of the time series imaging files, please contact us with regards to example data with which to test the script out on.

Tracking data (except actual images due to file size) used for figures and data within the paper are available from http://socooper.com/downloads/NucliTrack.zip. This package contains sub-folders, each associated with a specific figure panel.

Mathematical Modelling

This folder provides the mathematical model used to simulate data shown in Fig. 6 and S7. The following versions are available:

• Barr2017_DynamicsOfP21_SBtoolbox: Deterministic version of the model for the Systems Biology Toolbox 2 (now known as IQM Tools, http://www.intiquan.com/iqm-tools/) 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.
• Barr2017_DynamicsOfP21_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.
• Barr2017_DynamicsOfP21_SBML: Deterministic version of the model in the Systems Biology Markup Language (http://sbml.org/Main_Page), level 3 version 1. This file was created from the Copasi version of the model to provide compatibility with other software tools.
• Barr2017_DynamicsOfP21_Copasi_Deterministic: Deterministic version of the model for Copasi (http://copasi.org/). Simulating this file re-creates Fig. S7A.
• Barr2017_DynamicsOfP21_Copasi_Stochastic: Stochastic version of the model for Copasi (http://copasi.org/). Simulating this file provides a single stochastic realisation of the model. Stochastic simulations in the manuscript were, however, created with a custom-made MatLab implementation of the Stochastic Simulation Algorithm not provided here.