Paulevé, Loïc
2020-07-01
<p>These notebooks demonstrate Most Permissive Boolean Networks (<a href="http://dx.doi.org/10.1101/2020.03.22.998377">doi:10.1101/2020.03.22.998377</a>) on several case studies of biological networks.</p>
<p>They can be executed interactively within the <a href="http://colomoto.org/notebook">CoLoMoTo Docker</a> version <code>2020-07-01</code>:</p>
<ul>
<li>online, using myBinder service at <a href="https://mybinder.org/v2/zenodo/10.5281/zenodo.3936123/">https://mybinder.org/v2/zenodo/10.5281/zenodo.3936123/</a></li>
<li>or on your computer, provided you have <a href="https://docs.docker.com/get-docker/">Docker</a> and Python 3 installed:
<ol>
<li>download the notebooks individually from below, or from <a href="https://github.com/pauleve/MPBNs-SI-Notebooks/archive/main.zip">https://github.com/pauleve/MPBNs-SI-Notebooks/archive/main.zip</a> and extract the zip file</li>
<li>execute the following commands, where <code>notebooks</code> is the folder in which you extracted the notebooks:
<pre><code class="language-bash">sudo pip install -U colomoto-docker # you may have to use pip3 instead of pip
colomoto-docker -V 2020-07-01 --bind notebooks</code></pre>
</li>
</ol>
</li>
</ul>
<p>Visualize online:</p>
<ul>
<li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/MPBN%20applied%20to%20Bladder%20Tumorigenesis%20by%20Remy%20et%20al%202015.ipynb">MPBN applied to Bladder Tumorigenesis by Remy et al 2015.ipynb</a></li>
<li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/MPBN%20applied%20to%20T-Cell%20differentiation%20model%20by%20Abou-Jaoud%C3%A9%20et%20al.%202015.ipynb">MPBN applied to T-Cell differentiation model by Abou-Jaoudé et al. 2015.ipynb</a></li>
<li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/MPBN%20applied%20to%20Tumour%20invasion%20model%20by%20Cohen%20et%20al.%202015.ipynb">MPBN applied to Tumour invasion model by Cohen et al. 2015.ipynb</a></li>
<li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/I3FFL%20-%20compatible%20MPBNs.ipynb">I3FFL - compatible MPBNs.ipynb</a></li>
<li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/Scalability%20on%20large%20random%20BNs.ipynb">Scalability on large random BNs.ipynb</a></li>
</ul>
<p>The notebooks rely on the Python library <a href="https://github.com/pauleve/mpbn">mpbn</a>, see the documentation for usage and examples at <a href="https://mpbn.readthedocs.io/">https://mpbn.readthedocs.io</a></p>
https://doi.org/10.5281/zenodo.3936123
oai:zenodo.org:3936123
Zenodo
https://doi.org/10.5281/zenodo.3719059
https://doi.org/10.5281/zenodo.3719029
https://doi.org/10.5281/zenodo.3719018
https://doi.org/10.5281/zenodo.3715516
https://doi.org/10.5281/zenodo.3715210
https://doi.org/10.1101/2020.03.22.998377
https://doi.org/10.5281/zenodo.3719096
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Jupyter notebooks
Computational systems biology
Notebooks demonstrating Most Permissive Boolean Networks
info:eu-repo/semantics/other