Other Open Access

Notebooks demonstrating Most Permissive Boolean Networks

Paulevé, Loïc


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/bonesis-preview-20200701.zip"
      }, 
      "checksum": "md5:958161ca649ac91aad84b4dc89535dc7", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "bonesis-preview-20200701.zip", 
      "type": "zip", 
      "size": 32183
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/Dockerfile"
      }, 
      "checksum": "md5:e8b15575e2de6864d270debc5a408bf5", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "Dockerfile", 
      "type": "", 
      "size": 198
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/I3FFL%20-%20compatible%20MPBNs.ipynb"
      }, 
      "checksum": "md5:adfa465fb4fec42ff75070e80fbdb5ad", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "I3FFL - compatible MPBNs.ipynb", 
      "type": "ipynb", 
      "size": 10369
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/MPBN%20applied%20to%20Bladder%20Tumorigenesis%20by%20Remy%20et%20al%202015.ipynb"
      }, 
      "checksum": "md5:e3d7e324f7cf193bf79402c7c70716a4", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "MPBN applied to Bladder Tumorigenesis by Remy et al 2015.ipynb", 
      "type": "ipynb", 
      "size": 116162
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/MPBN%20applied%20to%20T-Cell%20differentiation%20model%20by%20Abou-Jaoud%C3%A9%20et%20al.%202015.ipynb"
      }, 
      "checksum": "md5:24f93796a30972d8711200cdaa0cd3bf", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "MPBN applied to T-Cell differentiation model by Abou-Jaoud\u00e9 et al. 2015.ipynb", 
      "type": "ipynb", 
      "size": 191554
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/MPBN%20applied%20to%20Tumour%20invasion%20model%20by%20Cohen%20et%20al.%202015.ipynb"
      }, 
      "checksum": "md5:2d4c1f697ff8ee844b4acfdb52ffc66c", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "MPBN applied to Tumour invasion model by Cohen et al. 2015.ipynb", 
      "type": "ipynb", 
      "size": 70882
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc/Scalability%20on%20large%20random%20BNs.ipynb"
      }, 
      "checksum": "md5:64b4aaa5b22b12933b30ca5e43f0e248", 
      "bucket": "115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
      "key": "Scalability on large random BNs.ipynb", 
      "type": "ipynb", 
      "size": 50310
    }
  ], 
  "owners": [
    43554
  ], 
  "doi": "10.5281/zenodo.3936123", 
  "stats": {
    "version_unique_downloads": 132.0, 
    "unique_views": 101.0, 
    "views": 115.0, 
    "version_views": 225.0, 
    "unique_downloads": 61.0, 
    "version_unique_views": 187.0, 
    "volume": 8429167.0, 
    "version_downloads": 185.0, 
    "downloads": 94.0, 
    "version_volume": 39893126.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.3936123", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.3719096", 
    "bucket": "https://zenodo.org/api/files/115cc3d9-886f-43a8-98a2-aea370d4b1cc", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.3719096.svg", 
    "html": "https://zenodo.org/record/3936123", 
    "latest_html": "https://zenodo.org/record/3936123", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.3936123.svg", 
    "latest": "https://zenodo.org/api/records/3936123"
  }, 
  "conceptdoi": "10.5281/zenodo.3719096", 
  "created": "2020-07-08T20:57:47.791949+00:00", 
  "updated": "2020-07-08T21:22:37.644871+00:00", 
  "conceptrecid": "3719096", 
  "revision": 3, 
  "id": 3936123, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.3936123", 
    "description": "<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>\n\n<p>They can be executed interactively within the <a href=\"http://colomoto.org/notebook\">CoLoMoTo Docker</a> version <code>2020-07-01</code>:</p>\n\n<ul>\n\t<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>\n\t<li>or on your computer, provided you have <a href=\"https://docs.docker.com/get-docker/\">Docker</a> and Python 3 installed:\n\t<ol>\n\t\t<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>\n\t\t<li>execute the following commands, where <code>notebooks</code> is the folder in which you extracted the notebooks:\n\t\t<pre><code class=\"language-bash\">sudo pip install -U colomoto-docker # you may have to use pip3 instead of pip\ncolomoto-docker -V 2020-07-01 --bind notebooks</code></pre>\n\t\t</li>\n\t</ol>\n\t</li>\n</ul>\n\n<p>Visualize online:</p>\n\n<ul>\n\t<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>\n\t<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-Jaoud&eacute; et al. 2015.ipynb</a></li>\n\t<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>\n\t<li><a href=\"https://nbviewer.jupyter.org/urls/zenodo.org/record/3936123/files/I3FFL%20-%20compatible%20MPBNs.ipynb\">I3FFL - compatible MPBNs.ipynb</a></li>\n\t<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>\n</ul>\n\n<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>", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "title": "Notebooks demonstrating Most Permissive Boolean Networks", 
    "relations": {
      "version": [
        {
          "count": 2, 
          "index": 1, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "3719096"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "3936123"
          }
        }
      ]
    }, 
    "keywords": [
      "Jupyter notebooks", 
      "Computational systems biology"
    ], 
    "publication_date": "2020-07-01", 
    "creators": [
      {
        "orcid": "0000-0002-7219-2027", 
        "affiliation": "CNRS/LaBRI", 
        "name": "Paulev\u00e9, Lo\u00efc"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "other", 
      "title": "Other"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3719059", 
        "relation": "isSupplementedBy", 
        "resource_type": "dataset"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3719029", 
        "relation": "isSupplementedBy", 
        "resource_type": "dataset"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3719018", 
        "relation": "isSupplementedBy", 
        "resource_type": "dataset"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3715516", 
        "relation": "isCompiledBy", 
        "resource_type": "software"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3715210", 
        "relation": "isSupplementedBy", 
        "resource_type": "software"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.1101/2020.03.22.998377", 
        "relation": "isSupplementTo", 
        "resource_type": "publication-preprint"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.3719096", 
        "relation": "isVersionOf"
      }
    ]
  }
}
225
185
views
downloads
All versions This version
Views 225115
Downloads 18594
Data volume 39.9 MB8.4 MB
Unique views 187101
Unique downloads 13261

Share

Cite as