def synthesize_with_dreal(crn):
derivatives = [{"variable": 'PThree', "order": 1, "is_variance": False, "name": "PThree_dot"}]
flow = crn.flow(False, derivatives)
#specification_dreal = [('', '', 'PThree > 0.4 '), ('', '', 'PThree < 0.3')]
specification_dreal = [('','PThree_dot >= 0','and (PThree_dot < 0.01) (PThree > 0.4) '),('','PThree_dot <= 0','(PThree < 0.3)')]
#specification_dreal = [('', 'PThree_dot >= 0', '(and (PThree > 0.3) (PThree_dot = 0))'), ('', 'PThree_dot <= 0', '(and (PThree >= 0)(PThree < 0.1))')]
drh = iSATParser.constructdReal(crn, specification_dreal, flow, other_constraints='(PThree < 0.4)',scale_factor=1)
with open('sixreactionnetwork.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./sixreactionnetwork.drh", dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./sixreactionnetwork_1_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulationdreal.png", t = linspace(0, 10, 1000))
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = [{"variable": 'PThreeStar', "order": 1, "is_variance": False, "name": "PThreeStar_dot"}]
flow = crn.flow(False, derivatives)
specification_dreal = [('', '', '(inputTime > 20)'),
('', '(PThreeStar_dot > 0)', '(and (PThreeStar > 0.5)(abs(PThreeStar_dot) < 0.01))'),
('', 'abs(PThreeStar_dot) < 0.01', 'inputTime > 100')]
#flow = crn.flow(False, derivatives)
#specification_dreal = [('', '', '')]
drh = iSATParser.constructdReal(crn, specification_dreal, flow, max_time=350, other_constraints='', scale_factor=1)
with open('switch.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./switch.drh", dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1, max_depth=len(specification_dreal))
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./switch_2_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 300, 1000))
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = []
flow = crn.flow(False, derivatives)
specification_dreal = [('', '', '(X < 0.1)')]
drh = iSATParser.constructdReal(crn, specification_dreal, flow)
with open('simple.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./simple.drh", dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0)
for file_name in result_files:
print("\n\n")
# print(sc.getCRNValues(file_name))
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulationdreal.png")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
isLNA = False
derivatives = []
#specification_dreal = [('','','')]
specification_dreal = [('', '', '(and (inputTime > 70)(cIts > 10))')]
flow = crn.flow(False, derivatives)
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=100)
with open('toggleswitch.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./toggleswitch.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./toggleswitch_0_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 100, 200)) # mode_times=all_vals["time"])
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def exampleParametricCRN():
X = Species('X')
Y = Species('Y')
B = Species('B')
k1 = RateConstant('k_1', 0.1, 10)
k2 = RateConstant('k_2', 0.1, 10)
k3 = RateConstant('k_3', 0.1, 10)
reaction1 = Reaction([Term(LambdaChoice([X, Y], 1), 1),
Term(Y, 1)], [Term(X, 1), Term(B, 1)], k1)
reaction2 = Reaction(
[Term(LambdaChoice([X, Y], 2), 1),
Term(X, Choice(0, 0, 2))], [Term(Y, 1), Term(B, 1)], k2)
reaction3 = Reaction([Term(X, 1), Term(B, 1)],
[Term(X, 1), Term(X, 1)], k3)
reaction4 = Reaction([Term(X, 1), Term(B, 1)],
[Term(X, 1), Term(X, 1)], k3)
crn = CRNSketch([reaction1, reaction2, reaction3], [reaction4], [])
isLNA = False
derivatives = []
specification = []
flow = crn.flow(isLNA, derivatives)
return iSATParser.constructdReal(crn, specification, flow)
def exampleLotkaOscillator(solver='iSAT'):
A = Species('A')
B = Species('B')
k1 = RateConstant('k_1', 0.01, 2)
k2 = RateConstant('k_2', 0.01, 2)
k3 = RateConstant('k_3', 0.01, 2)
reaction1 = Reaction([Term(A, 1)], [Term(A, 2)], k1)
reaction2 = Reaction([Term(A, 1), Term(B, 1)], [Term(B, 2)], k2)
reaction3 = Reaction([Term(B, 1)], [], k3)
crn = CRNSketch([reaction1, reaction2, reaction3], [], [])
isLNA = False
derivatives = [{
"variable": 'A',
"order": 1,
"is_variance": False,
"name": "A_dot"
}, {
"variable": 'B',
"order": 1,
"is_variance": False,
"name": "B_dot"
}]
specification = [(0.1, 'A_dot = 0'), (0.2, 'A_dot < 0 or A_dot > 0'),
(0.3, 'A_dot = 0')]
flow = crn.flow(isLNA, derivatives)
if solver is 'iSAT':
return iSATParser.constructISAT(crn, specification, flow)
elif solver is 'dReal':
return iSATParser.constructdReal(crn, specification, flow)
def getProblem(crn_sketch_string, crn_code, specification_string):
if specification_string:
input_species = get_input_species(specification_string)
isLNA, requiredDerivatives, specification = construct_specification(
specification_string)
else:
input_species = []
isLNA = False
requiredDerivatives = []
specification = []
crn = {}
constraints = []
if crn_code:
exec(crn_code)
else:
crn_details = CRNbuilder(crn_sketch_string, input_species)
crn = CRNSketch(crn_details.required_reactions,
crn_details.optional_reactions, input_species)
constraints = crn_details.constraints
flow = crn.flow(isLNA, requiredDerivatives)
isat_problem, modes = iSATParser.constructISAT(crn, specification, flow,
constraints), specification
dreal_problem, modes = iSATParser.constructdReal(
crn, specification, flow, constraints), specification
return isat_problem, dreal_problem, flow, crn
def synthesize_with_dreal(crn):
derivatives = []
flow = crn.flow(True, derivatives)
specification_dreal = [('', 'varA >= A', 'A > 0.3')]
#specification_dreal = [('','','')]
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=20)
with open('superpoisson.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./superpoisson.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./superpoisson_0_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions,
parametrised_flow,
plot_name=file_name +
"-simulationdreal.png",
t=linspace(0, 20, 100),
lna=True)
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn):
derivatives = [{
"variable": 'PThreeStar',
"order": 1,
"is_variance": False,
"name": "PThreeStar_dot"
}]
flow = crn.flow(False, derivatives)
# specification_dreal = [('', '', 'PThree > 0.4 '), ('', '', 'PThree < 0.3')]
# specification_dreal = [('','','(PThreeStar > 0.5) '),('','','(PThreeStar < 0.4)')]
# specification_dreal = [('', 'PThree_dot >= 0', '(and (PThree > 0.3) (PThree_dot = 0))'), ('', 'PThree_dot <= 0', '(and (PThree >= 0)(PThree < 0.1))')]
# specification_dreal = [('', '', '(and ((inputTime > 100)(PThreeStar < 0.75))'),
# ('', '', '(PThreeStar > 0.9)')]
specification_dreal = [('', '', 'inputTime > 20'),
('', 'PThreeStar_dot < 0', '(PThreeStar_dot=0)'),
('', 'PThreeStar_dot > 0', '(PThreeStar_dot=0)'),
('', 'PThreeStar_dot < 0', 'PThreeStar_dot = 0'),
('', 'PThreeStar_dot = 0', 'inputTime > 100')]
#flow = crn.flow(False, [])
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=350,
other_constraints='',
scale_factor=1)
with open('topology365.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./topology365.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./topology365_0_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 300, 1000),
hidden_variables="POne,POneStar,PTwo,PTwoStar,PThree")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def synthesize_with_dreal(crn, name, specification_dreal, result_file):
derivatives = [{
"variable": 'PThreeStar',
"order": 1,
"is_variance": False,
"name": "PThreeStar_dot"
}]
flow = crn.flow(False, derivatives)
#flow = crn.flow(False, derivatives)
#specification_dreal = [('', '', '')]
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=350 / SF,
other_constraints='',
scale_factor=SF)
with open(name, 'w') as file:
file.write(drh)
#sc = SolverCallerDReal(name, dreal_path="/code/dReal-3.16.06.02-linux/bin/dReach")
sc = SolverCallerDReal(
name, dreal_path="/code/dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in [result_file]: # TODO: remove ths aegument
print file_name
# './inverted-bell_3_0.smt2.proof'
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 350, 1000),
mode_times=all_vals["time"],
hidden_variables="POne,POneStar,PTwo,PTwoStar,PThree")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def exampleParametricCRN_complete():
X = Species('X', initial_max=5)
Y = Species('Y', initial_value=12)
B = Species('B')
reaction1 = Reaction([(LambdaChoice([X, Y], 1), 1), (Y, 1)], [(X, 1),
(B, 1)],
RateConstant('k_1', 1, 2))
reaction2 = Reaction([(LambdaChoice([X, Y], 2), 1), (X, Choice(0, 0, 3))],
[(Y, 1), (B, 1)], RateConstant('k_2', 1, 2))
reaction3 = Reaction([(X, 1), (B, 1)], [(X, 1), (X, 1)],
RateConstant('k_3', 1, 2))
reaction4 = Reaction([(X, 1), (B, 1)], [(X, 1), (X, 1)],
RateConstant('k_4', 1, 2))
input1 = InputSpecies(
"Input1",
sympify(
"0.1*t + 54.2735055776743*exp(-(0.04*t - 2.81375654916915)**2) + 35.5555607722356/(1.04836341039216e+15*(1/t)**10.0 + 1)"
), 15)
reaction5 = Reaction([Term(input1, 1)], [Term(B, 1)],
RateConstant('k_input', 1, 2))
isLNA = False
derivatives = [{
"variable": 'X',
"order": 1,
"is_variance": False,
"name": "X_dot"
}, {
"variable": 'X',
"order": 2,
"is_variance": False,
"name": "X_dot_dot"
}, {
"variable": 'X',
"order": 2,
"is_variance": True,
"name": "covX_dot_dot"
}]
#derivatives = []
specification = [(0, 'X = 0'), (0.5, 'X = 0.5'), (1, 'X = 0')]
crn = CRNSketch([reaction1, reaction2, reaction3, reaction5], [reaction4],
[input1])
flow = crn.flow(isLNA, derivatives)
crn.get_cost()
return iSATParser.constructdReal(crn, specification, flow, costFunction='')
def synthesize_with_dreal(crn):
derivatives = [{
"variable": 'L3p',
"order": 1,
"is_variance": False,
"name": "L3p_dot"
}, {
"variable": 'L3p',
"order": 2,
"is_variance": False,
"name": "L3p_dot_dot"
}]
flow = crn.flow(False, derivatives)
specification_dreal = [('', '(and (L3p_dot >= 0)(L3p_dot_dot >= 0))',
'(and (L3p_dot_dot = 0)(B > 4/SF))'),
('', '(and (L3p_dot >= 0)(L3p_dot_dot <= 0))', '')]
#specification_dreal = [('','','')]
drh = iSATParser.constructdReal(crn,
specification_dreal,
flow,
max_time=50 / SF,
scale_factor=SF)
with open('phosphorelay.drh', 'w') as file:
file.write(drh)
sc = SolverCallerDReal("./phosphorelay.drh",
dreal_path="../dReal-3.16.09.01-linux/bin/dReach")
result_files = sc.single_synthesis(cost=0, precision=0.1)
for file_name in result_files:
vals, all_vals = sc.getCRNValues('./phosphorelay_1_0.smt2.proof')
initial_conditions, parametrised_flow = sc.get_full_solution(
crn, flow, all_vals, scale_factor=SF)
print("Initial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(
initial_conditions,
parametrised_flow,
plot_name=file_name + "-simulationdreal.png",
t=linspace(0, 50 / SF, 100),
mode_times=all_vals["time"],
hidden_variables="B")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulationdreal.csv", sol, delimiter=",")
def exampleToggleSwitch():
lacl = Species('lacl')
clts = Species('clts')
empty_1 = Species('empty_1')
empty_2 = Species('empty_2')
empty_3 = Species('empty_3')
empty_4 = Species('empty_4')
a_2 = RateConstant('a_2', 0.1, 2)
a_4 = RateConstant('a_4', 0.1, 2)
alpha_1 = RateConstant('alpha_1', 0.1, 5)
alpha_2 = RateConstant('alpha_2', 0.1, 5)
beta = RateConstant('beta', 0.1, 5)
gamma = RateConstant('gamma', 0.1, 5)
#a_1 = RateConstant(str(alpha_1.symbol / 1 + (clts.symbol ** beta.symbol)), 0, 5)
# a_3 = RateConstant(str(alpha_2.symbol / 1 + (lacl.symbol ** gamma.symbol)), 0, 5)
a_1 = RateConstant('a_1', 0, 5)
a_3 = RateConstant('a_3', 0, 5)
input1 = InputSpecies(
"Input1",
sympify(
"0.1*t + 54.2735055776743*exp(-(0.04*t - 2.81375654916915)**2) + 35.5555607722356/(1.04836341039216e+15*(1/t)**10.0 + 1)"
), 15)
reaction1 = Reaction([Term(empty_1, 1)], [Term(lacl, 1)], a_1)
reaction2 = Reaction([Term(lacl, 1)], [Term(empty_2, 1)], a_2)
reaction3 = Reaction([Term(empty_3, 1)], [Term(clts, 1)], a_3)
reaction4 = Reaction([Term(clts, 1)], [Term(empty_4, 1)], a_4)
crn = CRNSketch([reaction1, reaction2, reaction3, reaction4], [], [input1])
isLNA = False
derivatives = []
specification = []
flow = crn.flow(isLNA, derivatives)
return iSATParser.constructdReal(crn, specification, flow)
def mixedMMExample():
A = Species('A')
g = Species('g')
Ag = Species('Ag')
Out = Species('Out')
vAmax = RateConstant('VA_max', 0.5, 5)
vBmax = RateConstant('VB_max', 0.5, 5)
vConstant = RateConstant('vConstant', 0.5, 0.5)
reaction1 = MichaelisMentenReaction([(A, 1), (g, 1)], [(Ag, 1), (A, 1)],
vAmax, vConstant)
reaction2 = MichaelisMentenReaction([(Ag, 1)], [(A, 1), (g, 1)], vBmax,
vConstant)
reaction3 = Reaction([Term(Ag, 1)], [Term(Out, 1)],
RateConstant('k1', 0.1, 5))
reaction4 = Reaction([Term(Out, 1)], [], RateConstant('k2', 0.1, 5))
isLNA = True
derivatives = [{
"variable": 'Out',
"order": 1,
"is_variance": False,
"name": "dOut"
}, {
"variable": 'Out',
"order": 2,
"is_variance": False,
"name": "ddOut"
}]
#Here specification should be when second derivative is 0 we want variance of O < certain threshold
#specification = [(0, 'O = 0'), (0.5, 'O < 0.5'), (1, 'O > 1')]
specification = [('', '', 'ddOut = 0'), ('', 'covAg > 10'),
('', 'Out > 1')]
crn = CRNSketch([reaction1, reaction2, reaction3, reaction4], [], [])
flow = crn.flow(isLNA, derivatives)
return flow, iSATParser.constructdReal(crn, specification, flow)
