Supporting data for "Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision" by Chevalier et al., 2020

<p>Code, data, and notebooks used for the synthesis and simulations of ensembles of Boolean networks for the tumor invasion model introduced in <a href="https://doi.org/10.1371/journal.pcbi.1004571">(Cohen et al, 2015)</a></p> <p>Visualize online:</p> <ul> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3938904/files/Simulations%20-%20Mutant%20analysis.ipynb">Simulations - Mutant analysis.ipynb </a></li> <li>&nbsp;<a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3938904/files/Tumour%20-%20Synthesis%20with%20BoNesis.ipynb">Tumour - Synthesis with BoNesis.ipynb</a></li> </ul> <p>The notebooks can be executed within the <a href="http://colomoto.org/notebook">CoLoMoTo Docker</a> image 2020-07-01:</p> <pre><code>pip install -U colomoto-docker colomoto-docker -V 2020-07-01 --bind . </code></pre> <p>The synthesis additionally requires executing the following command (within the Docker image):</p> <pre><code>pip install --user bonesis-preview-20200514.zip </code></pre> <p>The ensembles have been generated with the following commands.</p> <pre><code>python synthesis.py synthesis --exact-pkn --globalfps python synthesis.py synthesis --exact-pkn --globalfps --mutant p53 --mutant NICD </code></pre> <p>&nbsp;</p> <ul> </ul>