coupledboolnet allows users to create and simulate single or multicellular-coupled Boolean networks with different interaction rules (lienar threshold or Ising model).
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.
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Edit
bnsettings.pyfor extensive paramter of control with boolean networks. Options include perturbation, temperatureT, interaction strengthh. -
Run methods from
runanalysis2.pyseparately for visualization tools of the simulation outcomes. -
coupledboolent/kamiakcontains scripts for running on SLURM supported clusters.
- Run on Kamiak: Done
- Visualization script: Done
- Python Docstring