Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"
Authors/Creators
- 1. Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
- 2. LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
- 3. Freie Universität Berlin, Institute of Mathematics, D-14195 Berlin, Germany
- 4. Univ. Bordeaux, Bordeaux INP, CNRS, LaBRI, UMR5800, F-33400 Talence, France
Description
This record contains notebooks and Docker image for reproducing the learning of Boolean controls in regulated metabolic networks, and the case study presented in the CMSB 2021 conference proceeding article "Learning Boolean controls in regulated metabolic networks: a case-study".
Visualize notebooks online:
Notebooks can be executed interactively within the Docker image bioasp/boolean-caspo-flux:cmsb2021 which extends the CoLoMoTo Docker version 2021-02-01.
Alternatively, they can be executed without any installation at https://mybinder.org/v2/zenodo/10.5281/zenodo.5070151/.
The Docker image can be executed as follows:
docker pull bioasp/boolean-caspo-flux:cmsb2021
docker run -it --rm -p 8888:8888 bioasp/boolean-caspo-flux:cmsb2021
then point your browser to http://127.0.0.1:8888.
The image can be imported using the command docker load with the image file provided in this record:
docker load -i image.tar.gzor with the donodo command available at https://github.com/pauleve/donodo:
pip install -U donodo
donodo pull 10.5281/zenodo.5070151Files
CaseStudy-Inference.ipynb
Files
(887.3 MB)
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md5:e2deb9df24d0f6f980e1a5f6e2619a25
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265.4 kB | Preview Download |
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md5:cb2ed6219b2310f9a3ef1ba0096abdb0
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md5:ebac366f66a8b9c7c1c60bd6db038bc8
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206.7 kB | Preview Download |
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md5:b4e8633d0433ace1ecccd6226bb5012e
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2.5 kB | Download |
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md5:61ee75aeacae18727db419b4c9a42544
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74.8 MB | Download |
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md5:670e3cbeb95ee549df484685d8411efe
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554 Bytes | Download |
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md5:28882619fbc34b9ff4c50e01217761ed
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812.0 MB | Download |
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md5:b607c42edad87dea3baa7d8965d6fedd
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10.7 kB | Download |
Additional details
Related works
- Is derived from
- Dataset: https://github.com/bioasp/boolean-caspo-flux (URL)
Funding
- Agence Nationale de la Recherche
- BNeDiction - Predictive Boolean Network Ensembles ANR-20-CE45-0001