example: classifiers for phenotypes

To run the script use:

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

example: steady states

To run the script use:

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

bnet format

Syntax for .bnet files and classifier definition is

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

requirements

The main requirement is SAGE:

• https://www.sagemath.org/

docker

build image:

docker build -t rschwieger .

run image:

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

about the algorithm

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