ERK activity during early blastocyst development

This repository contains the code necessary to reproduce the simulation and analysis shown in the reasearch article titled: "TBD".

Data analysis

All data analysis is done in Python and contained within the folder data_analysis in this repository. In there you will find the two files that reproduce the results shown in Figure 5 and Supplementary Figure 1. The files that reproduce these results are:

• remove_debris.ipynb: Jupyter notebook with the instructions to compute the size threshold separating debris from nuclei.
• quantification.ipynb: Jupyter notebook with the instructions to segment nuclei and quantify the fluorescence using the resulting masks.

All segmentations rely on StarDist and the tilesegment package. See https://github.com/dsb-lab/tilesegment for details about installation.

Simulations

Modeling is performed using mainly the Julia programming language and contained in the models/models folder within this repository. A results folder is predefined in models/results so the user can save there the resulting figures of the simulations that reproduce the results of the article. In this work, we study 9 models, each contained in its specific folder in models/models/MODEL_NAME. The models shown are the following.

• bistability: Simple bistability circuit shown in Supplementary Figure 2.
• tristability: Simple tristability circuit shown in Supplementary Figure 2.

These two first models are written in Python. The rest are all written in Julia.

• saiz_hadjantonakis_2020: 3d version of the model shown in Saiz et al. (2020). The model results are shown in Figure 2 of this work.
• saiz_hadjantonakis_2020_FGFko: in silico FGF knock out of the previous model. The model results are shown in Figure 3 and Supplementary Figure 3.
• ERK1_saiz_extension: Direct extension of the previous two models which includes explicit ERK dyncamics. The model results are shown in Figure 4.
• ERK2_additive: Alternative ERK model with additive inhibition of NANOG by GATA6 and ERK. The model results are shown in Figure 6.
• ERK2_multiplicative: Alternative ERK model with multiplicative inhibition of NANOG by GATA6 and ERK. The model results are shown in Figure 7.
• ERK3_FGFR2: Extension of the multiplicative model which includes explicit dynamics of the FGFR2. The model results are shown in Figure 8.
• ERK3_homeostasis: Analysis of signaling range, role of initial conditions and model homeostasis of the previous model. The model results are shown in Figure 9 and Figure 10.