Coupled Boolean Networks:

coupledboolnet allows users to create and simulate single or multicellular-coupled Boolean networks with different interaction rules (lienar threshold or Ising model).

How to use

Users supply connectivty value k from command line:

python -m coupleboolnet [k-value]

By default, if importsavedata = True, coupledboolnet searches specfied directory path under coupledboolnet/data/ directory.

Otherwise, the default setting is a tissue of 10-by-10 cells with 10-genes with perturbation, and Ising interaction.

Contents

• Edit bnsettings.py for extensive paramter of control with boolean networks. Options include perturbation, temperature T, interaction strength h.

• Run methods from runanalysis2.py separately for visualization tools of the simulation outcomes.

• coupledboolent/kamiak contains scripts for running on SLURM supported clusters.

Work to be done:

1. Run on Kamiak: Done
2. Visualization script: Done
3. Python Docstring