def setUp(self):
self.vm1 = m.Species("vm1", 1e-6)
self.vm1_down = m.OrientedSpecies(self.vm1, m.Orient.down)
self.sm1 = m.Species("sm1", 1e-6, surface=True)
self.sm1_up = m.OrientedSpecies(self.sm1, m.Orient.up)
self.vm2 = m.Species("vm2", 1e-6)
self.vm2_down = m.OrientedSpecies(self.vm2, m.Orient.down)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", volume=False, dc=1e-6)
c = m.Species("c", volume=False, dc=1e-6)
a_mix = (a, m.Orient.mix)
b_up = (b, m.Orient.up)
c_up = (c, m.Orient.up)
bimol_irrev = m.Reaction([a_mix, b_up], [c_up], rate=1e4)
box = m.import_obj(Path("./box.obj"))
sim = m.Simulation(dt=1e-6, meshes=[box], reactions=[bimol_irrev])
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", dc=1e-6)
c = m.Species("c", dc=1e-6)
a_mix = (a, m.Orient.mix)
b_mix = (b, m.Orient.mix)
c_mix = (c, m.Orient.mix)
bimol_irrev = m.Reaction([a_mix, b_mix], [c_mix], rate=0)
box = m.create_box("box", 1.0, (0, 0, 0))
sim = m.Simulation(dt=1e-6, meshes=[box], reactions=[bimol_irrev])
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
for i in range(100):
offs = 1e6
bimol_irrev.rate = math.sin(i * 0.1) * offs + offs
sim.run_iteration()
def main():
a = m.Species("a", dc=1e-6)
reg = m.Region("tube_reg", tube.reg_indices)
tube_obj = m.MeshObject("tube", tube.verts, tube.faces, [reg])
mesh_objs = [tube_obj]
sim = m.Simulation(dt=1e-6, meshes=mesh_objs)
sim.create_molecules_reg(a, reg, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", dc=1e-6)
c = m.Species("c", dc=1e-6)
a_mix = (a, m.Orient.mix)
b_mix = (b, m.Orient.mix)
c_mix = (c, m.Orient.mix)
unimol1 = m.Reaction([a_mix], [b_mix], rate=1e4)
unimol2 = m.Reaction([a_mix], rate=1e4)
bimol_irrev = m.Reaction([a_mix, b_mix], [c_mix], rate=1e4)
bimol_rev = m.Reaction([a_mix, b_mix], [c_mix], reversible=True, rate=1e4)
rxns = [unimol1, unimol2, bimol_irrev, bimol_rev]
box = m.import_obj(Path("./box.obj"))
sim = m.Simulation(dt=1e-6, meshes=[box], reactions=rxns)
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
plane_top = m.create_plane("top", 1.0, (0, 0, 0.1))
plane_bottom = m.create_plane("bottom", 1.0, (0, 0, -0.1))
mesh_objs = [plane_top, plane_bottom]
sim = m.Simulation(dt=1e-6, meshes=mesh_objs)
for i in range(-10, 11):
sim.create_molecule(a, (i*0.1, 0, 0))
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", dc=1e-6)
c = m.Species("c", dc=1e-6)
a_mix = (a, m.Orient.mix)
b_mix = (b, m.Orient.mix)
c_mix = (c, m.Orient.mix)
bimol_irrev = m.Reaction([a_mix, b_mix], [c_mix], rate=1e4, name="rxn")
box = m.create_box("box", 1.0, (0, 0, 0))
count_a_box = m.CountMolecules(a, box)
count_a_rxn = m.CountReaction(bimol_irrev, box)
sim_counts = [count_a_box, count_a_rxn]
sim = m.Simulation(dt=1e-6,
meshes=[box],
reactions=[bimol_irrev],
counts=sim_counts)
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", volume=False, dc=1e-6)
box = m.create_box("box", 1.0, (0, 0, 0))
sim = m.Simulation(dt=1e-6, meshes=[box])
sim.create_molecules_reg(a,
box.regions["top"],
100,
conc_dens=True,
orient=m.Orient.up)
sim.run_iterations(100)
def create_species_from_dm(data_model: Dict[str, Any]) -> Dict[str, m.Species]:
""" Create a dictionary of Species from a CB data model """
logging.info("Creating species from data model")
species_dm_list = data_model['mcell']['define_molecules']['molecule_list']
species_dict = {}
for species_dm in species_dm_list:
species_name = species_dm['mol_name']
dc = float(species_dm['diffusion_constant'])
species_type = species_dm['mol_type']
surface = False
if species_type == '2D':
surface = True
species_dm = m.Species(species_name, dc, surface)
species_dict[species_name] = species_dm
return species_dict
def main():
a = m.Species("a", dc=1e-6)
a_up = (a, m.Orient.up)
a_down = (a, m.Orient.down)
transp_a = m.SurfaceProperty("transp_a", m.SP.transp, a_down)
absorb_a = m.SurfaceProperty("absorb_a", m.SP.absorb, a_down)
clamp_a = m.SurfaceProperty("clamp_a", m.SP.clamp, a_up, clamp_val=1e-8)
box = m.create_box("box", 1.0, (0, 0, 0))
box.add_surface_property(transp_a, box.regions["left"])
box.add_surface_property(absorb_a, box.regions["right"])
box.add_surface_property(clamp_a, box.regions["top"])
box.add_surface_property(absorb_a, box.regions["top"])
sim = m.Simulation(dt=1e-6, meshes=[box])
sim.create_molecules_obj(a, box, 100)
sim.run_iterations(100)
def create_my_model():
#Some parameters:
V = 0.125*1e-15 # um^3 -> liters
NA = 6.022e23/1e6
#Rate Constants (The numbers used here are taken from the SBML file available online)
k_on1C = 4/(NA*V) #1/uM 1/s
k_off1C = 40 #1/s (10-70)
k_on2C = 10/(NA*V) #1/uM 1/s
k_off2C = 9.25 #1/s (8.5-10)
k_on1N = 100/(NA*V) #1/uM 1/s
k_off1N = 2500 #1/s
k_on2N = 150/(NA*V) #1/uM 1/s
k_off2N = 750 #1/s
k_onCaM1C1N = 3.3/(NA*V) #1/uM 1/s
k_offCaM1C1N = 3.4 #1/s
k_onCaMKII = 50/(NA*V) #1/uM 1/s
k_offCaMKII = 60 #1/s
k_pCaM1C1N = 0.094 #1/s
# Add some geometries
a001 = pymcell.Geometry.fromFile("a001.ply")
print(a001)
C = pymcell.Sites(
states = [0,1,2]
)
N = pymcell.Sites(
states = [0,1,2]
)
Y286 = pymcell.Sites(
states = ['0','P']
)
b_site = pymcell.Sites(
states = [0,1]
int bond_N = 0
) # the way I envision this whenver bond_N > 1 (optional feature, present only for binding sutes) states becomes 1
ca = pymcell.Species(
name="ca",
diff_const=10.0
)
CaM = pymcell.Species(
name = "CaM",
diff_const =10.0,
sites = [C,N,b_site]
)
CaMKII = pymcell.Species(
name = "CaM",
diff_const =10.0,
sites = [b_site,Y286,rb_site,lb_site]
)
Complex = pymcell.Complex(
name = "Complex",
components = [],
diff_const =10.0, # calculated from components?
)
bng_rxn = BNGRxn(...)
rxn_volume = pymcell.Rxn(
name="first rxn",
fwd_rate=k_on1C,
bkwd_rate=k_off1C,
reactants=[
CaM(sites(C[0],b_stie.state[0])),
ca
],
products=[
CaM(sites(C[1],b_stie.state[0]))
]
)
rxn_volume = pymcell.Rxn(
name="second rxn",
fwd_rate=k_on2C,
bkwd_rate=k_off2C,
reactants=[
CaM(sites(C[1],b_stie.state[0])),
ca
],
products=[
CaM(sites(C[2],b_stie.state[0]))
]
)
rxn_volume = pymcell.Rxn(
name="third rxn",
fwd_rate=k_on1N,
bkwd_rate=k_off1N,
reactants=[
CaM(sites(N[0],b_stie.state[0])),
ca
],
products=[
CaM(sites(N[1],b_stie.state[0]))
]
)
rxn_volume = pymcell.Rxn(
name="fourth rxn",
fwd_rate=k_on2N,
bkwd_rate=k_off2N,
reactants=[
CaM(sites(N[1],b_stie.state[0])),
ca
],
products=[
CaM(sites(N[2],b_stie.state[0]))
]
)
rxn_volume = pymcell.Rxn(
name="fifth rxn",
fwd_rate=k_onCaM1C1N,
bkwd_rate=k_offCaM1C1N,
reactants=[
CaM(sites(C[1],N[1],b_stie.state[0])),
CaMKII(sites(b_stie.state[0],Y286['0']))
],
products=[
Complex(components = [CaM(sites(C[1],N[1],b_site.N_bond=1)),CaMKII(sites(b_site.N_bond=1,Y286['0']))])
]
)
rxn_volume = pymcell.Rxn(
name="sixth rxn",
fwd_rate=k_onCaMKII,
bkwd_rate=k_offCaMKII
reactants=[
Complex(components = [
CaMKII(sites(b_site.state[1],Y286['0'],rb_stie.state[0],lb_stie.state[0])),
])
Complex(components =[
CaMKII(sites(b_site.state[1],rb_stie.state[0],lb_stie.state[0]))
])
]
products=[
Complex(components = [
CaMKII(sites(b_site.state[1],Y286['0'],lb_site.bond_N=1,rb_stie.state[0])),
CaMKII(sites(b_site.state[1],lb_stie.state[0],rb_site.bond_N=1))
])
]
)
rxn_volume = pymcell.Rxn(
name="seventh rxn",
fwd_rate=k_pCaM1C1N,
reactants=[
Complex(components = [
CaMKII(sites(b_site.state[1],Y286['0'],lb_site.bond_N=1)),
CaM(sites(C[1],N[1],b_site.bond_N=2)),
CaMKII(sites(b_site.bond_N=2,Y286['0'],rb_site.bond_N=1))
])
]
products=[
Complex(components = [
CaM,
CaMKII(sites(b_site.state[1],Y286['0'],lb_site.bond_N=1)),
CaM(sites(C[1],N[1],b_site.bond_N=2)),
CaMKII(sites(b_site.bond_N=2,Y286['P'],rb_site.bond_N=1))
])
]
)
# Create releases
release_1 = pymcell.ReleaseSite(
name="Ca",
type=pymcell.RELEASE_TYPE.OBJECT,
species=ca,
quantity=10*(NA*V),
release_probability=1,
object=a001.get_volume_region("dendritic_spine")
)
release_2 = pymcell.ReleaseSite(
name="CaM",
type=pymcell.RELEASE_TYPE.OBJECT,
species=CaM(sites(C[0],N[0],b_stie.state[0])),
quantity=30*(NA*V),
release_probability=1,
object=a001.get_volume_region("dendritic_spine")
)
release_3 = pymcell.ReleaseSite(
name="CaMKII",
type=pymcell.RELEASE_TYPE.OBJECT,
species=CaMKII(sites(b_stie.state[0],Y286['0'],rb_stie.state[0],lb_stie.state[0])),
quantity=80*(NA*V),
release_probability=1,
object=a001.get_volume_region("dendritic_spine")
)
# Finally: add all that to a model
m = pymcell.Model()
m.add_geometry(a001)
m.add_species(ca)
m.add_species(CaM)
m.add_species(CaMKII)
m.add_rxn(rxn_volume)
m.add_release_site(release_1,release_2,release_3)
m.add_rxn(bng_rxn)
return m
def create_my_model():
# Add some geometries
a001 = pymcell.Geometry.fromFile("a001.ply")
print(a001)
# Make a species
pmca_p0 = pymcell.Species(
name="pmca_p0",
diff_const=10.0
)
pmca_po.set_diff_const(5)
ca = pymcell.Species(
name="ca",
diff_const=10.0
)
pmca_p1 = pymcell.Species(
name="pmca_p1",
diff_const=10.0
)
bng_rxn = BNGRxn(...)
# Make a surface reaction
# pmca_p0' + ca, <-> pmca_p1'
rxn_surface = pymcell.Rxn(
name="first rxn",
fwd_rate=1.0,
bkwd_rate=2.0,
reactants=[
pymcell.oriented_species(pmca_p0, pymcell.ORIENT.UP),
pymcell.oriented_species(ca, pymcell.ORIENT.DOWN)
],
products=[
pymcell.oriented_species(pmca_p1, pymcell.ORIENT.UP)
]
)
# Make a volume reaction
# calbindin_h0m0 + ca <-> calbindin_h1m0
rxn_volume = pymcell.Rxn(
name="second rxn",
fwd_rate=1.0,
bkwd_rate=2.0,
reactants=[
calbindin_h0m0,
ca
],
products=[
calbindin_h1m0
]
)
# Create releases
release_1 = pymcell.ReleaseSite(
name="pmca_p0_pre_rel",
type=pymcell.RELEASE_TYPE.OBJECT,
species=pmca_p0,
quantity=100,
release_probability=1,
object=a001.get_surface_region("axon_membrane")
)
# Finally: add all that to a model
m = pymcell.Model()
m.add_geometry(a001)
m.add_species(pmca_p0)
m.add_species(ca)
m.add_species(pmca_p1)
m.add_rxn(rxn_volume)
m.add_rxn(rxn_surface)
m.add_release_site(release_1)
m2 = pymcell.Model()
m2.add_geometry(a001)
m2.add_species(pmca_p0)
m2.add_species(ca)
m2.add_species(pmca_p1)
m2.add_rxn(rxn_volume)
m2.add_rxn(rxn_surface)
m2.add_release_site(release_1)
m.add_rxn(bng_rxn)
return m
def main():
world = m.MCellSim(seed=1)
world.set_time_step(time_step=1e-5)
world.set_iterations(iterations=1000)
world.enable_logging()
world.silence_notifications()
world.set_output_freq(1)
slow_dc = 1e-9
fast_dc = 1e-5
# define species
vm1 = m.Species("vm1", fast_dc)
vm2 = m.Species("vm2", fast_dc)
vm3 = m.Species("vm3", slow_dc)
sm_list = []
for i in range(1, 11):
sm_list.append(m.Species("sm{}".format(i), fast_dc, surface=True))
sm1 = sm_list[0]
sm2 = sm_list[1]
spec_orient_list = [sm.up() for sm in sm_list]
all_mols = sm_list + [vm1, vm2, vm3]
world.add_species(all_mols)
# define reaction
rxn = m.Reaction(sm1.up(), sm2.down(), 1e3, name="create_sm2")
world.add_reaction(rxn)
# create torus object
torus_obj = m.MeshObj(
"Torus", t.vert_list, t.face_list, translation=(0, 0, 0))
torus_reg = m.SurfaceRegion(torus_obj, 'half', t.surf_reg_face_list)
world.add_geometry(torus_obj)
# create box object
box_obj = m.MeshObj(
"Box", b.vert_list, b.face_list, translation=(0, 0, 0))
box_reg = m.SurfaceRegion(box_obj, 'top', b.surf_reg_face_list)
world.add_geometry(box_obj)
# create surface class to absorb vm1
# sc = m.SurfaceClass(SC.absorb, sm1.mix())
# world.assign_surf_class(sc, torus_reg)
# world.assign_surf_class_to_all_surface_mols("abs_all_surfs", SC.absorb, torus_reg)
world.assign_surface_property_to_all_mols(
"abs_all_vols", SC.absorb, torus_reg, moltype=MolType.surface_mols)
# release vm1, vm2, and sm1 molecules into/onto torus
vm1_torus_rel = m.ObjectRelease(vm1, number=1000, mesh_obj=torus_obj)
world.release(vm1_torus_rel)
vm2_torus_rel = m.ObjectRelease(vm2, number=1000, mesh_obj=torus_obj)
world.release(vm2_torus_rel)
sm1_torus_rel = m.ObjectRelease(sm1.up(), number=1000, region=torus_reg)
world.release(sm1_torus_rel)
# release vm3 molecules in a line (list based release)
vm3_pos = [(x*0.01, 0, 0) for x in range(-5, 5)]
vm3_list_release = m.ListRelease(vm3, vm3_pos)
world.release(vm3_list_release)
# release sm molecules in a line on top of box (list based release)
sm_pos = [(x*0.01, 0, 0.1) for x in range(-5, 5)]
sm_list_release = m.ListRelease(spec_orient_list, sm_pos)
world.release(sm_list_release)
# pos_vec3 = m.Vector3()
# diam_vec3 = m.Vector3(0.015, 0.015, 0.015)
# world.create_release_site(vm1, 100, "spherical", diam_vec3=diam_vec3)
# viz and reaction data
world.add_viz(all_mols)
world.add_count(vm1, torus_obj)
world.add_count(vm2, torus_obj)
world.add_count(sm1, torus_obj)
# set partitions
world.add_partitions('x', -1.3, 1.3, 0.05)
world.add_partitions('y', -1.3, 1.3, 0.05)
world.add_partitions('z', -0.275, 0.275, 0.05)
# run the simulation! :)
# for i in range(iterations+1):
# vm3_count = world.get_species_count(vm3, torus_obj)
# if (vm3_count > 50):
# world.modify_rate_constant(rxn, 1e12)
# world.run_iteration()
world.run_sim()
world.end_sim()
def create_vector3(x=0., y=0., z=0.):
v = m.vector3()
v.x = x
v.y = y
v.z = z
return v
m.initialize_electric_field()
m.update_electric_field(new_electric_field)
world = m.MCellSim(2)
world.set_time_step(dt)
world.set_iterations(iterations=N)
spec = m.Species("Ca", 4e-6)
spec.z = 2
world.add_species(spec)
shape = 'spherical'
quantity = 10000
diam = create_vector3()
pos = create_vector3()
world.create_release_site(spec, quantity, shape, pos, diam)
f_n = 'results/output_' + str(mode) + '/'
world.add_count(spec, folder_name=f_n)
world.add_viz([spec], step=1, folder_name=f_n)
for i in range(world._iterations):
world.run_iteration()
world.end_sim()
def main():
a = m.Species("a", dc=1e-6)
sim = m.Simulation(dt=1e-6)
sim.create_molecules_shape(a, 100, (0, 0, 0))
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
box = m.create_box("box", 1.0, (0, 0, 0))
sim = m.Simulation(dt=1e-6)
sim.create_molecules_obj(a, box, 100)
sim.run_iterations(100)
def create_my_model():
# Add some geometries
a001 = pymcell.Geometry.fromFile("a001.ply")
print(a001)
C = pymcell.Sites(
states = [0,1,2]
)
N = pymcell.Sites(
states = [0,1,2]
)
Y286 = pymcell.Sites(
states = ['0','P']
)
b_site = pymcell.Sites(
states = [0,1]
)
# # Make a species
# pmca_p0 = pymcell.Species(
# name="pmca_p0",
# diff_const=10.0
# )
# pmca_po.set_diff_const(5)
ca = pymcell.Species(
name="ca",
diff_const=10.0
)
# pmca_p1 = pymcell.Species(
# name="pmca_p1",
# diff_const=10.0
# )
CaM = pymcell.Species(
name = "CaM",
diff_const =10.0,
states = [C,N,b_site]
)
CaMKII = pymcell.Species(
name = "CaM",
diff_const =10.0,
states = [b_site,Y286]
)
Complex = pymcell.Complex(
name = "Complex",
components = [],
diff_const =10.0, # calculated from components?
)
bng_rxn = BNGRxn(...)
# Make a surface reaction
# pmca_p0' + ca, <-> pmca_p1'
# rxn_surface = pymcell.Rxn(
# name="first rxn",
# fwd_rate=1.0,
# bkwd_rate=2.0,
# reactants=[
# pymcell.oriented_species(pmca_p0, pymcell.ORIENT.UP),
# pymcell.oriented_species(ca, pymcell.ORIENT.DOWN)
# ],
# products=[
# pymcell.oriented_species(pmca_p1, pymcell.ORIENT.UP)
# ]
# )
# Make a volume reaction
# calbindin_h0m0 + ca <-> calbindin_h1m0
# rxn_volume = pymcell.Rxn(
# name="second rxn",
# fwd_rate=1.0,
# bkwd_rate=2.0,
# reactants=[
# calbindin_h0m0,
# ca
# ],
# products=[
# calbindin_h1m0
# ]
rxn_volume = pymcell.Rxn(
name="third rxn",
fwd_rate=1.0,
bkwd_rate=2.0,
reactants=[
CaM(states(C[0],b_site[0])),
ca
],
products=[
CaM(states(C[1],b_site[0]))
]
)
rxn_volume = pymcell.Rxn(
name="third rxn",
fwd_rate=1.5,
bkwd_rate=1.5,
reactants=[
CaM(states(C[1],b_site[0])),
ca
],
products=[
CaM(states(C[2],b_site[0]))
]
)
rxn_volume = pymcell.Rxn(
name="fourth rxn",
fwd_rate=1.0,
bkwd_rate=2.0,
reactants=[
CaM(states(C[0],b_site[0])),
CaMKII(states(b_site[0],Y286[0]))
],
products=[
Complex(components = [CaM(states(C[1],b_site[1])),CaMKII(states(b_site[1],Y286[0]))])
]
)
rxn_volume = pymcell.Rxn(
name="fourth rxn",
fwd_rate=1.0,
reactants=[
Complex(components = [
CaM,
CaMKII(states(b_site[1],Y286[0],d_site[1])),
CaM(states(C[1],N[2],b_site[1])),
CaMKII(states(b_site[1],Y286[0],d_site[1]))
])
]
products=[
Complex(components = [
CaM,
CaMKII(states(b_site[1],Y286[0],d_site[1])),
CaM(states(C[1],N[2],b_site[1])),
CaMKII(states(b_site[1],Y286[P],d_site[1]))
])
]
)
# Create releases
release_1 = pymcell.ReleaseSite(
name="pmca_p0_pre_rel",
type=pymcell.RELEASE_TYPE.OBJECT,
species=pmca_p0,
quantity=100,
release_probability=1,
object=a001.get_surface_region("axon_membrane")
)
release_2 = CaM.ReleaseSite(
name="pmca_p0_pre_rel",
type=pymcell.RELEASE_TYPE.OBJECT,
species=CaM(CaM_states(C[0],N[0],Y286[0])),
quantity=100,
release_probability=1,
object=a001.get_volume_region("dendritic_spine")
)
# Finally: add all that to a model
m = pymcell.Model()
m.add_geometry(a001)
m.add_species(pmca_p0)
m.add_species(ca)
m.add_species(pmca_p1)
m.add_rxn(rxn_volume)
m.add_rxn(rxn_surface)
m.add_release_site(release_1)
m2 = pymcell.Model()
m2.add_geometry(a001)
m2.add_species(pmca_p0)
m2.add_species(ca)
m2.add_species(pmca_p1)
m2.add_rxn(rxn_volume)
m2.add_rxn(rxn_surface)
m2.add_release_site(release_1)
m.add_rxn(bng_rxn)
return m