def test4():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | B3 | C1 | C2 | C3 | {
"D": str(D),
"radius": str(radius)
}
with reaction_rules():
A1 + B1_ > B2 | 0.04483455086786913 > A1 + B1 | 1.35
B2 > A2 + B1 | 1.5
A2 + B1_ > B3 | 0.09299017957780264 > A2 + B1 | 1.73
B3 > A3 + B1 | 15.0
A3 + C1 > C2 | 0.04483455086786913 > A3 + C1 | 1.35
C2 > A2 + C1 | 1.5
A2 + C1 > C3 | 0.09299017957780264 > A2 + C1 | 1.73
C3 > A1 + C1 | 15.0
m = get_model()
w1 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w1.bind_to(m)
sim1 = meso.MesoscopicSimulator(w1)
w2 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
w2.bind_to(m)
sim2 = spatiocyte.SpatiocyteSimulator(w2)
# w2 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
# w2.bind_to(m)
# sim2 = egfrd.EGFRDSimulator(w2)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2', 'A3'))
ev1.add(('C1', 'C2', 'C3'))
ev1.borrow('B1', 'B1_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2', 'B3'))
owner.set_value(Species("A1"), 120)
owner.set_value(Species("B1"), 30)
owner.set_value(Species("C1"), 30)
owner.initialize()
logger = Logger(owner,
("A1", "A2", "A3", "B1", "B2", "B3", "C1", "C2", "C3"))
logger.add("B1_", w1)
logger.log()
while owner.step(1):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test3():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | B3 | {
"D": str(D), "radius": str(radius)}
with reaction_rules():
A1 == A2 | (1.0, 1.0)
B1 == B2 | (1.0, 1.0)
A2 + B2_ > B3 | 1.0 / 30.0
B3 > A2 + B2 | 1.0
m = get_model()
w1 = gillespie.GillespieWorld(edge_lengths)
w1.bind_to(m)
sim1 = gillespie.GillespieSimulator(w1)
# w2 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
# w2.bind_to(m)
# sim2 = meso.MesoscopicSimulator(w2)
# w2 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
# w2.bind_to(m)
# sim2 = spatiocyte.SpatiocyteSimulator(w2)
# w2 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
# w2.bind_to(m)
# sim2 = egfrd.EGFRDSimulator(w2)
w2 = ode.ODEWorld(edge_lengths)
w2.bind_to(m)
sim2 = ode.ODESimulator(w2)
sim2.set_dt(0.01)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2'))
ev1.borrow('B2', 'B2_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2', 'B3'))
owner.set_value(Species("A1"), 60)
owner.set_value(Species("B1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "B1", "B2", "B3"))
logger.add("B2_", w1)
logger.log()
while owner.step(10):
# while owner.step(50):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test3():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | B3 | {"D": str(D), "radius": str(radius)}
with reaction_rules():
A1 == A2 | (1.0, 1.0)
B1 == B2 | (1.0, 1.0)
A2 + B2_ > B3 | 1.0 / 30.0
B3 > A2 + B2 | 1.0
m = get_model()
w1 = gillespie.GillespieWorld(edge_lengths)
w1.bind_to(m)
sim1 = gillespie.GillespieSimulator(w1)
# w2 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
# w2.bind_to(m)
# sim2 = meso.MesoscopicSimulator(w2)
# w2 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
# w2.bind_to(m)
# sim2 = spatiocyte.SpatiocyteSimulator(w2)
# w2 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
# w2.bind_to(m)
# sim2 = egfrd.EGFRDSimulator(w2)
w2 = ode.ODEWorld(edge_lengths)
w2.bind_to(m)
sim2 = ode.ODESimulator(w2)
sim2.set_dt(0.01)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2'))
ev1.borrow('B2', 'B2_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2', 'B3'))
owner.set_value(Species("A1"), 60)
owner.set_value(Species("B1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "B1", "B2", "B3"))
logger.add("B2_", w1)
logger.log()
while owner.step(10):
# while owner.step(50):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test4():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | B3 | C1 | C2 | C3 | {"D": str(D), "radius": str(radius)}
with reaction_rules():
A1 + B1_ > B2 | 0.04483455086786913 > A1 + B1 | 1.35
B2 > A2 + B1 | 1.5
A2 + B1_ > B3 | 0.09299017957780264 > A2 + B1 | 1.73
B3 > A3 + B1 | 15.0
A3 + C1 > C2 | 0.04483455086786913 > A3 + C1 | 1.35
C2 > A2 + C1 | 1.5
A2 + C1 > C3 | 0.09299017957780264 > A2 + C1 | 1.73
C3 > A1 + C1 | 15.0
m = get_model()
w1 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w1.bind_to(m)
sim1 = meso.MesoscopicSimulator(w1)
w2 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
w2.bind_to(m)
sim2 = spatiocyte.SpatiocyteSimulator(w2)
# w2 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
# w2.bind_to(m)
# sim2 = egfrd.EGFRDSimulator(w2)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2', 'A3'))
ev1.add(('C1', 'C2', 'C3'))
ev1.borrow('B1', 'B1_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2', 'B3'))
owner.set_value(Species("A1"), 120)
owner.set_value(Species("B1"), 30)
owner.set_value(Species("C1"), 30)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "A3", "B1", "B2", "B3", "C1", "C2", "C3"))
logger.add("B1_", w1)
logger.log()
while owner.step(1):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test4():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | {"D": str(D), "radius": str(radius)}
with reaction_rules():
A1 + B1_ > B2 | 0.04483455086786913 > B1 + A2 | 1.35
B2 > B1 + A1 | 1.5
m = get_model()
w1 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w1.bind_to(m)
sim1 = meso.MesoscopicSimulator(w1)
# w2 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
# w2.bind_to(m)
# sim2 = spatiocyte.SpatiocyteSimulator(w2)
w2 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
w2.bind_to(m)
sim2 = egfrd.EGFRDSimulator(w2)
w1.add_molecules(Species("A1"), 120)
w2.add_molecules(Species("B1"), 60)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2'))
ev1.borrow('B1', 'B1_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2'))
owner.initialize()
logger = Logger(owner, ("A1", "A2", "B1", "B2"))
logger.add("B1_", w1)
logger.log()
while owner.step(1):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test4():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | {"D": str(D), "radius": str(radius)}
with reaction_rules():
A1 + B1_ > B2 | 0.04483455086786913 > B1 + A2 | 1.35
B2 > B1 + A1 | 1.5
m = get_model()
w1 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w1.bind_to(m)
sim1 = meso.MesoscopicSimulator(w1)
# w2 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
# w2.bind_to(m)
# sim2 = spatiocyte.SpatiocyteSimulator(w2)
w2 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
w2.bind_to(m)
sim2 = egfrd.EGFRDSimulator(w2)
w1.add_molecules(Species("A1"), 120)
w2.add_molecules(Species("B1"), 60)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2'))
ev1.borrow('B1', 'B1_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2'))
owner.initialize()
logger = Logger(owner, ("A1", "A2", "B1", "B2"))
logger.add("B1_", w1)
logger.log()
while owner.step(1):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test5():
edge_lengths = Real3(1, 1, 1)
with reaction_rules():
A1 == A2 | (1.0, 1.0)
B1 == B2 | (1.0, 1.0)
A1 == B1 | (1.0, 1.0)
A2 + B2_ > C1 | 1.0 / 30.0
C1 > A2 + B2 | 1.0
m = get_model()
w1 = meso.MesoscopicWorld(edge_lengths, Integer3(3, 3, 3))
w1.bind_to(m)
sim1 = meso.MesoscopicSimulator(w1)
w2 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w2.bind_to(m)
sim2 = meso.MesoscopicSimulator(w2)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2', 'C1'))
ev1.borrow('B2', 'B2_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2'))
owner.set_value(Species("A1"), 120)
# owner.set_value(Species("A1"), 60)
# owner.set_value(Species("B1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "C1", "B1", "B2"))
logger.add('B2_', w1)
logger.log()
while owner.step(5):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.savefig()
logger.savetxt()
def test5():
edge_lengths = Real3(1, 1, 1)
with reaction_rules():
A1 == A2 | (1.0, 1.0)
B1 == B2 | (1.0, 1.0)
A1 == B1 | (1.0, 1.0)
A2 + B2_ > C1 | 1.0 / 30.0
C1 > A2 + B2 | 1.0
m = get_model()
w1 = meso.MesoscopicWorld(edge_lengths, Integer3(3, 3, 3))
w1.bind_to(m)
sim1 = meso.MesoscopicSimulator(w1)
w2 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w2.bind_to(m)
sim2 = meso.MesoscopicSimulator(w2)
owner = Coordinator()
ev1 = simulator_event(sim1)
ev1.add(('A1', 'A2', 'C1'))
ev1.borrow('B2', 'B2_')
owner.add_event(ev1)
owner.add_event(simulator_event(sim2)).add(('B1', 'B2'))
owner.set_value(Species("A1"), 120)
# owner.set_value(Species("A1"), 60)
# owner.set_value(Species("B1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "C1", "B1", "B2"))
logger.add('B2_', w1)
logger.log()
while owner.step(5):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.savefig()
logger.savetxt()
def test2():
edge_lengths = Real3(1, 1, 1)
with reaction_rules():
A1 == A2 | (1.0, 1.0)
E1 == E2 | (1.0, 1.0)
A1 == E1 | (1.0, 1.0)
m = get_model()
w1 = gillespie.GillespieWorld(edge_lengths)
w1.bind_to(m)
sim1 = gillespie.GillespieSimulator(w1)
w2 = ode.ODEWorld(edge_lengths)
w2.bind_to(m)
sim2 = ode.ODESimulator(w2)
owner = Coordinator()
owner.add_event(simulator_event(sim1)).add(('A1', 'A2'))
owner.add_event(ODEEvent(sim2, 0.01)).add(('E1', 'E2'))
owner.set_value(Species("A1"), 120)
# owner.set_value(Species("A1"), 60)
# owner.set_value(Species("E1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "E1", "E2"))
logger.add("A1", w2)
logger.log()
while owner.step(50):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.savefig()
logger.savetxt()
def test2():
edge_lengths = Real3(1, 1, 1)
with reaction_rules():
A1 == A2 | (1.0, 1.0)
E1 == E2 | (1.0, 1.0)
A1 == E1 | (1.0, 1.0)
m = get_model()
w1 = gillespie.GillespieWorld(edge_lengths)
w1.bind_to(m)
sim1 = gillespie.GillespieSimulator(w1)
w2 = ode.ODEWorld(edge_lengths)
w2.bind_to(m)
sim2 = ode.ODESimulator(w2)
owner = Coordinator()
owner.add_event(simulator_event(sim1)).add(('A1', 'A2'))
owner.add_event(ODEEvent(sim2, 0.01)).add(('E1', 'E2'))
owner.set_value(Species("A1"), 120)
# owner.set_value(Species("A1"), 60)
# owner.set_value(Species("E1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "E1", "E2"))
logger.add("A1", w2)
logger.log()
while owner.step(50):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.savefig()
logger.savetxt()
def test1():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | C1 | C2 | D1 | D2 | E1 | E2 | {
"D": str(D), "radius": str(radius)}
with reaction_rules():
A1 == A2 | (1.0, 1.0)
B1 == B2 | (1.0, 1.0)
C1 == C2 | (1.0, 1.0)
D1 == D2 | (1.0, 1.0)
E1 == E2 | (1.0, 1.0)
A1 == B1 | (1.0, 1.0)
A1 == C1 | (1.0, 1.0)
A1 == D1 | (1.0, 1.0)
A1 == E1 | (1.0, 1.0)
B1 == C1 | (1.0, 1.0)
B1 == D1 | (1.0, 1.0)
B1 == E1 | (1.0, 1.0)
C1 == D1 | (1.0, 1.0)
C1 == E1 | (1.0, 1.0)
D1 == E1 | (1.0, 1.0)
m = get_model()
w1 = gillespie.GillespieWorld(edge_lengths)
w1.bind_to(m)
sim1 = gillespie.GillespieSimulator(w1)
w2 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w2.bind_to(m)
sim2 = meso.MesoscopicSimulator(w2)
w3 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
w3.bind_to(m)
sim3 = spatiocyte.SpatiocyteSimulator(w3)
w4 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
w4.bind_to(m)
sim4 = egfrd.EGFRDSimulator(m, w4)
w5 = ode.ODEWorld(edge_lengths)
w5.bind_to(m)
sim5 = ode.ODESimulator(w5)
sim5.set_dt(0.01)
owner = Coordinator()
owner.add_event(simulator_event(sim1)).add(('A1', 'A2'))
owner.add_event(simulator_event(sim2)).add(('B1', 'B2'))
owner.add_event(simulator_event(sim3)).add(('C1', 'C2'))
owner.add_event(simulator_event(sim4)).add(('D1', 'D2'))
owner.add_event(simulator_event(sim5)).add(('E1', 'E2'))
owner.set_value(Species("A1"), 300)
# owner.set_value(Species("A1"), 60)
# owner.set_value(Species("B1"), 60)
# owner.set_value(Species("C1"), 60)
# owner.set_value(Species("D1"), 60)
# owner.set_value(Species("E1"), 60)
owner.initialize()
logger = Logger(owner, ("A1", "A2", "B1", "B2", "C1", "C2", "D1", "D2", "E1", "E2"))
logger.log()
while owner.step(3):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()
def test1():
D, radius = 1, 0.005
edge_lengths = Real3(1, 1, 1)
with species_attributes():
A1 | A2 | B1 | B2 | C1 | C2 | D1 | D2 | E1 | E2 | {
"D": str(D),
"radius": str(radius)
}
with reaction_rules():
A1 == A2 | (1.0, 1.0)
B1 == B2 | (1.0, 1.0)
C1 == C2 | (1.0, 1.0)
D1 == D2 | (1.0, 1.0)
E1 == E2 | (1.0, 1.0)
A1 == B1 | (1.0, 1.0)
A1 == C1 | (1.0, 1.0)
A1 == D1 | (1.0, 1.0)
A1 == E1 | (1.0, 1.0)
B1 == C1 | (1.0, 1.0)
B1 == D1 | (1.0, 1.0)
B1 == E1 | (1.0, 1.0)
C1 == D1 | (1.0, 1.0)
C1 == E1 | (1.0, 1.0)
D1 == E1 | (1.0, 1.0)
m = get_model()
w1 = gillespie.GillespieWorld(edge_lengths)
w1.bind_to(m)
sim1 = gillespie.GillespieSimulator(w1)
w2 = meso.MesoscopicWorld(edge_lengths, Integer3(9, 9, 9))
w2.bind_to(m)
sim2 = meso.MesoscopicSimulator(w2)
w3 = spatiocyte.SpatiocyteWorld(edge_lengths, radius)
w3.bind_to(m)
sim3 = spatiocyte.SpatiocyteSimulator(w3)
w4 = egfrd.EGFRDWorld(edge_lengths, Integer3(4, 4, 4))
w4.bind_to(m)
sim4 = egfrd.EGFRDSimulator(m, w4)
w5 = ode.ODEWorld(edge_lengths)
w5.bind_to(m)
sim5 = ode.ODESimulator(w5)
sim5.set_dt(0.01)
owner = Coordinator()
owner.add_event(simulator_event(sim1)).add(('A1', 'A2'))
owner.add_event(simulator_event(sim2)).add(('B1', 'B2'))
owner.add_event(simulator_event(sim3)).add(('C1', 'C2'))
owner.add_event(simulator_event(sim4)).add(('D1', 'D2'))
owner.add_event(simulator_event(sim5)).add(('E1', 'E2'))
owner.set_value(Species("A1"), 300)
# owner.set_value(Species("A1"), 60)
# owner.set_value(Species("B1"), 60)
# owner.set_value(Species("C1"), 60)
# owner.set_value(Species("D1"), 60)
# owner.set_value(Species("E1"), 60)
owner.initialize()
logger = Logger(
owner, ("A1", "A2", "B1", "B2", "C1", "C2", "D1", "D2", "E1", "E2"))
logger.log()
while owner.step(3):
if owner.last_event.event_kind == EventKind.REACTION_EVENT:
logger.log()
logger.log()
logger.savefig()
logger.savetxt()