Initial commit

README.md

+# Implementation notice of the deterministic model numeric resolution proposed by L. Darrigade and al (2021)
+
+This project propose the resolution of the deterministic model and its sensitivity analysis (SA). 
+We propose different Notebooks that will generate figures presented in the article and some complements. 
+More information such as equation and reminders of the article are provide in the notebooks.
+
+
+## Installation
+
+We assume that virtualenv is installed in your python environment. If it is not the case, execute the command in your shell
+
+```sh
+pip install virtualenv
+```
+
+To install the packages needed for the code execution, we will install a new python virtual environment
+
+```sh
+virtualenv -p python3 JOMB
+```
+
+Then, activate the virual environment
+
+```sh
+source JOMB/bin/activate
+```
+and install the required packages
+
+
+```sh
+pip install -r requirements.txt
+```
+
+You are now ready to open the jupyter notebooks 
+
+```sh
+jupyter notebook
+```
+
+Select in the list one of the two jupyter notebooks (either main_resolution_model.ipynb or main_sensitivity_analysis.ipynb)
+
+
+
+## Git folder composition 
+
+This git folder is composed of 2 Notebooks : 
+- main_resolution_model
+- main_sensitivity_analysis
+
+
+4 python files : 
+- util.py 
+- module_resolution.py
+- module_SA.py
+- module_kinetic_scheme.py
+
+3 folders 
+- TEX
+- SIMUS
+- backup_SA
+
+Installation requirements : 
+- requirements.txt 
+
+## Results backup
+Backups are present in the 3 different folders which allows the user to replicate the figures in the article without running the resolution and/or SA codes.
+In TEX you will find tex and png files of figures. Options are set to overwrite these backups (see Notebooks).  
+backup_SA is a folder containing results oh the sensitivity analysis perform for the article, this folder dialogues with main_sensitivity_analysis.
+And finaly SIMUS folder is used to dialogue with the notebook main_experiment_parameters and to store stochastic simulation results used to compare the two models. 
+
+
+## Warnings
+The SAFE library used in main_sensitivity_analysis notebook is open source however you need to ask for permission fist and download the library see : https://www.safetoolbox.info/. 
+Whitout permission user won't be able to use the previous notebook. 
+
+Moreover, different parallelization parts parts are present in the code (main_experiment_parameters & main_sensitivity_analysis), we advice users to be carefull when running cells specially for SA.
+Indeed results presented in the article used 90 CPU during about 24 hours (!). An example is proposed when performing a simplier SA (2 parameters).   
+
+
+

TEX/JOMB_cell_fate.tex

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+\pgfplotsset{compat=newest}
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TEX/JOMB_densities_article.tex

+\documentclass[convert]{standalone}
+\usepackage[utf8]{inputenc}
+\usepackage{pgfplots}
+\DeclareUnicodeCharacter{2212}{−}
+\usepgfplotslibrary{groupplots,dateplot}
+\usetikzlibrary{patterns,shapes.arrows}
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