def test_simple_assembly():
st1 = Activation(Agent('a'), Agent('b'))
st2 = Inhibition(Agent('a'), Agent('c'))
sa = SifAssembler([st1, st2])
sa.make_model()
assert len(sa.graph.nodes()) == 3
assert len(sa.graph.edges()) == 2
bn = sa.print_boolean_net()
model = boolean2.Model(text=bn_str, mode='async')
for i in range(nsim):
model.initialize()
model.iterate(steps=nsteps)
coll.collect(states=model.states, nodes=model.nodes)
avgs = coll.get_averages(normalize=True)
return avgs
if __name__ == '__main__':
# Build Boolean net for basic pathway
st = ac.load_statements('ras_pathway.pkl')
sa = SifAssembler(st)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway.sif')
bn_str = sa.print_boolean_net('ras_pathway_bn.txt')
# Build Boolean net for extended pathway
st_ext = ac.load_statements('ras_pathway_extension.pkl')
sa = SifAssembler(st + st_ext)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway_extension.sif')
bn_str = sa.print_boolean_net('ras_pathway_extension_bn.txt')
# Condition 1
off = []
on = ['GROWTH-FACTOR']
avgs = get_sim_avgs(bn_str, off=off, on=on)
jun_basic_noinh = avgs['JUN']
# Condition 2
model = boolean2.Model(text=bn_str, mode='async')
for i in range(nsim):
model.initialize()
model.iterate(steps=nsteps)
coll.collect(states=model.states, nodes=model.nodes)
avgs = coll.get_averages(normalize=True)
return avgs
if __name__ == '__main__':
# Build Boolean net for basic pathway
st = ac.load_statements('ras_pathway.pkl')
sa = SifAssembler(st)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway.sif')
bn_str = sa.print_boolean_net('ras_pathway_bn.txt')
# Build Boolean net for extended pathway
st_ext = ac.load_statements('ras_pathway_extension.pkl')
sa = SifAssembler(st + st_ext)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway_extension.sif')
bn_str = sa.print_boolean_net('ras_pathway_extension_bn.txt')
# Condition 1
off = []
on = ['GROWTH-FACTOR']
avgs = get_sim_avgs(bn_str, off=off, on=on)
jun_basic_noinh = avgs['JUN']
# Condition 2