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
, orginsim
object- filename in SBML-qual or boolSim format.
Returns a list of
colomoto.types.State
,colomoto.types.Hypercube
, orcolomoto.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
, orginsim
object- filename in SBML-qual or boolSim format.
init can be either a dict,
colomoto.types.State
,colomoto.types.Hypercube
, orcolomoto.types.HypercubeCollection
.Returns a
colomoto.types.State
,colomoto.types.Hypercube
, orcolomoto.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
, orcolomoto.types.HypercubeCollection
objects.Returns a
colomoto.types.State
,colomoto.types.Hypercube
, orcolomoto.types.HypercubeCollection
objects, orNone
, 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
, orcolomoto.types.HypercubeCollection
objects.Returns a
colomoto.types.State
,colomoto.types.Hypercube
, orcolomoto.types.HypercubeCollection
objects, orNone
, 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
, orcolomoto.types.HypercubeCollection
objects.Returns a
colomoto.types.State
,colomoto.types.Hypercube
, orcolomoto.types.HypercubeCollection
, depending on the result.