def make_path3mmh():
"""path3mmh: A reaction network of three reactions forming a linear pathway,
where all reactions have Michaelis-Menten-Haldane rate laws.
seed=0; atol=rtol=1e-12; intermediate_output=True success =False fail
"""
net = network.Network('path3mmh')
net.add_compartment(id='env')
net.add_compartment(id='cell')
net.add_species(id='C1',
compartment='env',
initial_value=2,
is_constant=True)
net.add_species(id='C2',
compartment='env',
initial_value=0.5,
is_constant=True)
net.add_species(id='X1', compartment='cell', initial_value=1)
net.add_species(id='X2', compartment='cell', initial_value=1)
net.add_reaction(id='R1',
eqn='C1<->X1',
ratelaw='V1f/K1C1*(C1-X1/KE1)/(1+C1/K1C1+X1/K1X1)',
p=OD([('V1f', 1), ('K1C1', 1), ('K1X1', 1), ('KE1', 5)]))
net.add_reaction(id='R2',
eqn='X1<->X2',
ratelaw='V2f/K2X1*(X1-X2/KE2)/(1+X1/K2X1+X2/K2X2)',
p=OD([('V2f', 1), ('K2X1', 1), ('K2X2', 1), ('KE2', 4)]))
net.add_reaction(id='R3',
eqn='X2<->C2',
ratelaw='V3f/K3X2*(X2-C2/KE3)/(1+X2/K3X2+C2/K3C2)',
p=OD([('V3f', 1), ('K3X2', 1), ('K3C2', 1), ('KE3', 1)]))
for KEid in ['KE1', 'KE2', 'KE3']:
net.set_var_optimizable(KEid, False)
net.compile()
return net
def make_cycle3mah():
"""cycle3mah: A reaction network of three reactions forming a cycle,
where all reactions have mass-action-Haldane rate laws.
"""
net = network.Network(id='cycle3mah')
net.add_compartment(id='env')
net.add_compartment(id='cell')
net.add_species(id='C1',
compartment='env',
initial_value=2,
is_constant=True)
net.add_species(id='C2',
compartment='env',
initial_value=2,
is_constant=True)
net.add_species(id='C3',
compartment='env',
initial_value=1,
is_constant=True)
net.add_species(id='X1', compartment='cell', initial_value=1)
net.add_species(id='X2', compartment='cell', initial_value=1)
net.add_reaction(id='R1',
eqn='C1+X1<->2 X2',
ratelaw='k1*(C1*X1-X2**2)',
p={'k1': 1})
net.add_reaction(id='R2',
eqn='C2+X2<->X1',
ratelaw='k2*(C2*X2-X1)',
p={'k2': 1})
net.add_reaction(id='R3', eqn='X2<->C3', ratelaw='k3*(X2-C3)', p={'k3': 1})
net.compile()
return net
def make_cycle4mah():
"""cycle4mah: A reaction network of four reactions forming a cycle,
where all reactions have mass-action-Haldane rate laws.
"""
net = network.Network(id='cycle4mah')
net.add_compartment(id='env')
net.add_compartment(id='cell')
net.add_species(id='C1',
compartment='env',
initial_value=2,
is_constant=True)
net.add_species(id='C2',
compartment='env',
initial_value=2,
is_constant=True)
net.add_species(id='C3',
compartment='env',
initial_value=1,
is_constant=True)
net.add_species(id='X1', compartment='cell', initial_value=0)
net.add_species(id='X2', compartment='cell', initial_value=0)
net.add_species(id='X3', compartment='cell', initial_value=0)
net.add_species(id='X4', compartment='cell', initial_value=0)
net.add_reaction(id='R1', eqn='C1+X1<->2 X2')
net.add_reaction(id='R2', eqn='X2+X3<->X1+X4')
net.add_reaction(id='R3', eqn='C2+X4<->X3')
net.add_reaction(id='R4', eqn='X2<->C3')
return net
def nets():
net1 = network.Network(id='net1')
net1.add_compartment(id='env')
net1.add_compartment(id='cell')
net1.add_species(id='C1', compartment='env', initial_value=2,
is_constant=True)
net1.add_species(id='C2', compartment='env', initial_value=1,
is_constant=True)
net1.add_species(id='X', compartment='cell', initial_value=0)
net1.add_reaction(id='R1', eqn='C1<->X', ratelaw='k1*(C1-X)', p={'k1':1})
net1.add_reaction(id='R2', eqn='X<->C2', ratelaw='k2*(X-C2)', p={'k2':2})
net1.compile()
net2 = network.Network(id='net2')
net2.add_compartment(id='env')
net2.add_compartment(id='cell')
net2.add_species(id='C1', compartment='env', initial_value=2,
is_constant=True)
net2.add_species(id='C2', compartment='env', initial_value=2,
is_constant=True)
net2.add_species(id='C3', compartment='env', initial_value=1,
is_constant=True)
net2.add_species(id='X1', compartment='cell', initial_value=0)
net2.add_species(id='X2', compartment='cell', initial_value=0)
net2.add_reaction(id='R1', eqn='C1+X1<->2 X2')
net2.add_reaction(id='R2', eqn='C2+X2<->X1')
net2.add_reaction(id='R3', eqn='X2<->C3')
net3 = network.Network(id='net3')
net3.add_compartment(id='env')
net3.add_compartment(id='cell')
net3.add_species(id='C1', compartment='env', initial_value=2,
is_constant=True)
net3.add_species(id='C2', compartment='env', initial_value=2,
is_constant=True)
net3.add_species(id='C3', compartment='env', initial_value=1,
is_constant=True)
net3.add_species(id='X1', compartment='cell', initial_value=0)
net3.add_species(id='X2', compartment='cell', initial_value=0)
net3.add_species(id='X3', compartment='cell', initial_value=0)
net3.add_species(id='X4', compartment='cell', initial_value=0)
net3.add_reaction(id='R1', eqn='C1+X1<->2 X2')
net3.add_reaction(id='R2', eqn='X2+X3<->X1+X4')
net3.add_reaction(id='R3', eqn='C2+X4<->X3')
net3.add_reaction(id='R4', eqn='X2<->C3')
return [net1, net2, net3]
def make_path2mah():
"""path2ma: A reaction network of two reactions forming a linear pathway,
where both reactions have mass-action-Haldane rate laws.
"""
net = network.Network(id='path2mah')
net.add_compartment(id='env')
net.add_compartment(id='cell')
net.add_species(id='C1',
compartment='env',
initial_value=2,
is_constant=True)
net.add_species(id='C2',
compartment='env',
initial_value=1,
is_constant=True)
net.add_species(id='X', compartment='cell', initial_value=0)
net.add_reaction(id='R1', eqn='C1<->X', ratelaw='k1*(C1-X)', p={'k1': 1})
net.add_reaction(id='R2', eqn='X<->C2', ratelaw='k2*(X-C2)', p={'k2': 2})
net.compile()
return net