To run the script use:

python3 groebner.py --bnet n7s3.bnet --phenotype "v4 & !v6"

To run the script use:

python3 groebner.py --bnet n7s3.bnet --steady-states

Syntax for .bnet files and classifier definition is

• | means disjunction
• & means conjunction
• ! means negation

The main requirement is SAGE:

• https://www.sagemath.org/

build image:

docker build -t rschwieger .

run image:

docker run -v $(pwd):/media -it rschwieger

The code implements the algorithm proposed in

Schwieger, Robert, Matías R. Bender, Heike Siebert, and Christian Haase. "Classifier construction in Boolean networks using algebraic methods." In International Conference on Computational Methods in Systems Biology, pp. 210-233. Springer, Cham, 2020. https://doi.org/10.1007/978-3-030-60327-4_12