Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"

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:

CaseStudy-Simulations.ipynb

CaseStudy-SearchSpace.ipynb

CaseStudy-Inference.ipynb

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.gz

or with the donodo command available at https://github.com/pauleve/donodo:

pip install -U donodo
donodo pull 10.5281/zenodo.5070151