import boolsim
from colomoto_jupyter import tabulate # for display

Computing attractors with boolSim

Input from a GINsim model

import ginsim

lrg = ginsim.load("https://zenodo.org/record/3719029/files/SuppMat_Model_Master_Model.zginml")

Downloading https://zenodo.org/record/3719029/files/SuppMat_Model_Master_Model.zginml

%time A = boolsim.attractors(lrg)
tabulate(A)

CPU times: user 26.4 ms, sys: 6.89 ms, total: 33.3 ms
Wall time: 1.92 s

	AKT1	AKT2	Apoptosis	CDH1	CDH2	CellCycleArrest	CTNNB1	DKK1	DNAdamage	ECMicroenv	EMT	ERK	GF	Invasion	Metastasis	Migration	miR200	miR203	miR34	NICD	p21	p53	p63	p73	SMAD	SNAI1	SNAI2	TGFbeta	TWIST1	VIM	ZEB1	ZEB2
5	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
1	0	0	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0
8	0	0	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0
3	0	0	1	1	0	1	0	0	1	1	0	0	0	0	0	0	1	0	0	0	1	0	1	1	0	0	0	1	0	0	0	0
0	0	0	1	1	0	1	0	0	1	1	0	0	0	0	0	0	1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0
2	0	1	0	0	1	1	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	1	1	1
4	0	1	0	0	1	1	0	0	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	1	1	1
6	0	1	0	0	1	1	0	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	1	1	1	1	1	1	1	1
7	0	1	0	0	1	1	0	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	1	1	1	1	1	1	1	1

Input from a minibn.BooleanNetwork object

from colomoto.minibn import BooleanNetwork

bn = BooleanNetwork({
    "a": "(a|b)&!(a&b)",
    "b": "(a|b)&!(a&b)"
})

a = boolsim.attractors(bn)
tabulate(a)

		a	b
1	0	0	0
0	0	0	1
	1	1	*

The attractor 1 is a fixed point:

a[1]

{'a': 0, 'b': 0}

The attractor 0 is a complex attractor, being represented as a list of hypercubes:

a[0]

[{'a': 0, 'b': 1}, {'a': 1, 'b': '*'}]