boolSim-python Documentation

This Python module is an interface to the software tools boolSim (https://www.vital-it.ch/research/software/boolSim) for the computation of attractors in synchronous and asynchronous Boolean Networks.

Examples can be found at https://nbviewer.jupyter.org/github/colomoto/boolSim-python/tree/main/examples/.

boolsim.attractors(bn, update_mode='asynchronous')

Compute the attractors of the given Boolean network bn using the update_mode (either "asynchronous" or "synchronous").

bn can be either:
  • colomoto.minibn.BooleanNetwork, biolqm, or ginsim object
  • filename in SBML-qual or boolSim format.

Returns a list of colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection, depending on the kind of attractors.

boolsim.reachable(bn, init, update_mode='asynchronous', max_iterations=0)

Compute the reachable states within the given Boolean network bn from the initial state(s) init, using update_mode (either "asynchronous" or "synchronous").

bn can be either:
  • colomoto.minibn.BooleanNetwork, biolqm, or ginsim object
  • filename in SBML-qual or boolSim format.

init can be either a dict, colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection.

Returns a colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection, depending on the result.

boolsim.difference(A, B, *C)

Perform difference between sets of states specified either as dict, colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection objects.

Returns a colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection objects, or None, depending on the result.

boolsim.intersection(A, B, *C)

Perform intersection between sets of states specified either as dict, colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection objects.

Returns a colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection objects, or None, depending on the result.

boolsim.union(A, B, *C)

Perform union between sets of states specified either as dict, colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection objects.

Returns a colomoto.types.State, colomoto.types.Hypercube, or colomoto.types.HypercubeCollection, depending on the result.