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Notebooks demonstrating Most Permissive Boolean Networks

Paulevé, Loïc


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  <identifier identifierType="DOI">10.5281/zenodo.3936123</identifier>
  <creators>
    <creator>
      <creatorName>Paulevé, Loïc</creatorName>
      <givenName>Loïc</givenName>
      <familyName>Paulevé</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-7219-2027</nameIdentifier>
      <affiliation>CNRS/LaBRI</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Notebooks demonstrating Most Permissive Boolean Networks</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Jupyter notebooks</subject>
    <subject>Computational systems biology</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-07-01</date>
  </dates>
  <resourceType resourceTypeGeneral="Other"/>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementedBy" resourceTypeGeneral="Dataset">10.5281/zenodo.3719018</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsCompiledBy" resourceTypeGeneral="Software">10.5281/zenodo.3715516</relatedIdentifier>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo" resourceTypeGeneral="Text">10.1101/2020.03.22.998377</relatedIdentifier>
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  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;These notebooks demonstrate Most Permissive Boolean Networks (&lt;a href="http://dx.doi.org/10.1101/2020.03.22.998377"&gt;doi:10.1101/2020.03.22.998377&lt;/a&gt;) on several case studies of biological networks.&lt;/p&gt;

&lt;p&gt;They can be executed interactively within the &lt;a href="http://colomoto.org/notebook"&gt;CoLoMoTo Docker&lt;/a&gt; version &lt;code&gt;2020-07-01&lt;/code&gt;:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;online, using myBinder service at &lt;a href="https://mybinder.org/v2/zenodo/10.5281/zenodo.3936123/"&gt;https://mybinder.org/v2/zenodo/10.5281/zenodo.3936123/&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;or on your computer, provided you have &lt;a href="https://docs.docker.com/get-docker/"&gt;Docker&lt;/a&gt; and Python 3 installed:
	&lt;ol&gt;
		&lt;li&gt;download the notebooks individually from below, or from &lt;a href="https://github.com/pauleve/MPBNs-SI-Notebooks/archive/main.zip"&gt;https://github.com/pauleve/MPBNs-SI-Notebooks/archive/main.zip&lt;/a&gt; and extract the zip file&lt;/li&gt;
		&lt;li&gt;execute the following commands, where &lt;code&gt;notebooks&lt;/code&gt; is the folder in which you extracted the notebooks:
		&lt;pre&gt;&lt;code class="language-bash"&gt;sudo pip install -U colomoto-docker # you may have to use pip3 instead of pip
colomoto-docker -V 2020-07-01 --bind notebooks&lt;/code&gt;&lt;/pre&gt;
		&lt;/li&gt;
	&lt;/ol&gt;
	&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Visualize online:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/MPBN%20applied%20to%20Bladder%20Tumorigenesis%20by%20Remy%20et%20al%202015.ipynb"&gt;MPBN applied to Bladder Tumorigenesis by Remy et al 2015.ipynb&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;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"&gt;MPBN applied to T-Cell differentiation model by Abou-Jaoud&amp;eacute; et al. 2015.ipynb&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/MPBN%20applied%20to%20Tumour%20invasion%20model%20by%20Cohen%20et%20al.%202015.ipynb"&gt;MPBN applied to Tumour invasion model by Cohen et al. 2015.ipynb&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/I3FFL%20-%20compatible%20MPBNs.ipynb"&gt;I3FFL - compatible MPBNs.ipynb&lt;/a&gt;&lt;/li&gt;
	&lt;li&gt;&lt;a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/Scalability%20on%20large%20random%20BNs.ipynb"&gt;Scalability on large random BNs.ipynb&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;The notebooks rely on the Python library &lt;a href="https://github.com/pauleve/mpbn"&gt;mpbn&lt;/a&gt;, see the documentation for usage and examples at &lt;a href="https://mpbn.readthedocs.io/"&gt;https://mpbn.readthedocs.io&lt;/a&gt;&lt;/p&gt;</description>
  </descriptions>
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