Growth factor-mediated coupling between lineage size and cell fate choice underlies robustness of mammalian development

N. Saiz, L. Mora-Bitria, S. Rahman, H. George, J.P. Herder, J. García-Ojalvo and A.-K. Hadjantonakis

This repository contains the code to reproduce the modeling figures of the paper by Saiz et al, published in eLife 2020;9:e56079 (doi: 10.7554/eLife.56079) and posted in bioRxiv (preprint 2019.12.27.889006). It includes the following:

• fig2b.ipynb: self-contained Jupyter notebook to generate the phase portrait shown in Figure 2b.
• fig2c.ipynb: Jupyter notebook to generate the lineage dynamics plot shown in Figure 2c. This notebook compiles and runs the C program embryo_v1.c, and plots the correspoding results. It requires the C compiler cc and the utility make, which are available by default in Linux, or by installing the Xcode development environment in Mac OS X.
• fig2e.ipynb: Jupyter notebook to generate the lineage dynamics plots shown in Figure 2e, using again the C program embryo_v1.c.
• fig3.ipynb: Jupyter notebook to generate the ESC addition plots shown in Figure 3, using in this case the C program embryo_v2.c.
• fig4.ipynb: Jupyter notebook to generate the ablation plots shown in Figure 4, using again the C program embryo_v1.c.