def synthesize_with_isat(crn):
#derivatives = []
derivatives = [{"variable": 'PThree', "order": 1, "is_variance": False, "name": "PThree_dot"}]
flow = crn.flow(False, derivatives)
# specification = [('', 'PThree_dot >= 0', '((PThree > 0.1) and (PThree_dot < 0.001))'), ('', 'PThree_dot <= 0', '')]
# specification = [('', '(K > 0.3) and (PThree_dot >= 0)', '(PThree_dot = 0)' ), ('', '(PThree_dot < 0)', '(K < 0.1) and (PThree_dot < 0)')]
# specification = [('', '', 'PThree > 0.4 '), ('', '', 'PThree < 0.3')]
#specification = [('','PThree_dot >= 0','PThree_dot = 0'),('','PThree_dot < 0','')]
# specification = [('','PThree_dot >= 0',' (PThree_dot = 0) and (PThree > 0.4) '),('','PThree_dot <= 0','(PThree < 0.3)')]
#
hys = iSATParser.constructISAT(crn, specification, flow, other_constraints='PThree < 0.4;',scale_factor=1)
with open('sixreactionnetwork.hys', 'w') as file:
file.write(hys)
sc = SolverCallerISAT("./sixreactionnetwork.hys", isat_path="../isat-ode-r2806-static-x86_64-generic-noSSE-stripped.txt")
result_files = sc.single_synthesis(cost=0, precision=0.1, msw=0.5)
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 + "-simulation.png", t = linspace(0, 10, 1000))
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulation.csv", sol, delimiter=",")
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 synthesize_with_isat(crn):
derivatives = []
flow = crn.flow(False, derivatives)
specification = [('', '', '(X < 0.1)')]
hys = iSATParser.constructISAT(crn, specification, flow)
with open('simple.hys', 'w') as file:
file.write(hys)
sc = SolverCallerISAT("./simple.hys", isat_path="../isat-ode-r2806-static-x86_64-generic-noSSE-stripped.txt")
result_files = sc.single_synthesis(cost=0)
for file_name in result_files:
vals, all_vals = sc.getCRNValues(file_name)
initial_conditions, parametrised_flow = sc.get_full_solution(crn, flow, all_vals)
print("\n\nInitial Conditions", initial_conditions)
print("Flow:", parametrised_flow)
t, sol, variable_names = sc.simulate_solutions(initial_conditions, parametrised_flow,
plot_name=file_name + "-simulation.png")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulation.csv", sol, delimiter=",")
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 AMExample():
X = Species('X')
Y = Species('Y')
B = Species('B')
reaction1 = Reaction([Term(X, 1), Term(Y, 1)],
[Term(X, 1), Term(B, 1)],
RateConstant('k_1', 0.1, 10))
reaction2 = Reaction([Term(Y, 1), Term(X, 1)],
[Term(Y, 1), Term(B, 1)],
RateConstant('k_2', 0.1, 10))
reaction3 = Reaction([Term(X, 1), Term(B, 1)],
[Term(X, 1), Term(X, 1)],
RateConstant('k_3', 0.1, 10))
reaction4 = Reaction([Term(Y, 1), Term(B, 1)],
[Term(Y, 1), Term(Y, 1)],
RateConstant('k_4', 0.1, 10))
crn = CRNSketch([reaction1, reaction2, reaction3, reaction4], [], [])
isLNA = False
derivatives = []
specification = []
flow = crn.flow(isLNA, derivatives)
return iSATParser.constructISAT(crn, specification, flow, costFunction='')
def synthesize_with_isat(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 = [('', '(L3p_dot >= 0) and (L3p_dot_dot >= 0)', '(L3p_dot_dot < 0.001)'),
# ('', '(L3p_dot >= 0) and (L3p_dot_dot <= 0)', '(L3p > 100)')]
#ok
specification = [('', '', '')]
flow = crn.flow(False, derivatives)
hys = iSATParser.constructISAT(crn, specification, flow, max_time=100)
with open('phosphorelay.hys', 'w') as file:
file.write(hys)
sc = SolverCallerISAT(
"./phosphorelay.hys",
isat_path="../isat-ode-r2806-static-x86_64-generic-noSSE-stripped.txt")
result_files = sc.single_synthesis(cost=0, precision=0.01, msw=0.05)
# result_files = ["./results/sixreactionstar_0_0.01-isat.txt"]
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 + "-simulation.png",
t=linspace(0, 100, 1000),
mode_times=all_vals["time"])
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulation.csv", sol, delimiter=",")
def synthesize_with_isat(crn):
# derivatives = []
derivatives = [{
"variable": 'PThreeStar',
"order": 1,
"is_variance": False,
"name": "PThreeStar_dot"
}]
flow = crn.flow(False, derivatives)
specification = [('', '', '')]
specification = [('', '', '(inputTime > 100) and (PThreeStar < 0.75)'),
('', '', '(PThreeStar > 0.9)')
] # try to capture an inverted-bellshape response
hys = iSATParser.constructISAT(crn,
specification,
flow,
max_time=350,
other_constraints='',
scale_factor=1)
# with open('sixreactionstar.hys', 'w') as file:
# file.write(hys)
sc = SolverCallerISAT(
"./sixreactionstar.hys",
isat_path="../isat-ode-r2806-static-x86_64-generic-noSSE-stripped.txt")
result_files = sc.single_synthesis(cost=0, precision=0.01, msw=0.05)
# result_files = ["./results/sixreactionstar_0_0.01-isat.txt"]
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 + "-simulation.png",
t=linspace(0, 350, 1000),
hidden_variables="POne,POneStar,PTwo,PTwoStar,PThree")
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulation.csv", sol, delimiter=",")
def michaelis_menten_example():
X = Species('X')
Y = Species('Y')
vmax = RateConstant('V_max', 0.1, 10)
km = RateConstant('K_m', 0.1, 10)
reaction = MichaelisMentenReaction([(X, 2)], [(Y, 3)], vmax, km)
derivatives = []
crn = CRNSketch([reaction], [], [])
flow = crn.flow(False, derivatives)
crn.get_cost()
return iSATParser.constructISAT(crn, [], flow, costFunction='')
def exampleJointAlternative():
X = Species('X', initial_max=5)
Y = Species('Y', initial_value=12)
B = Species('B')
reaction1 = Reaction([TermChoice(0, [(X, 2), (Y, 3)])], [(B, 1)],
RateConstant('k_1', 1, 2))
isLNA = False
derivatives = []
specification = [(0, 'X = 0'), (0.5, 'X = 0.5'), (1, 'X = 0')]
crn = CRNSketch([reaction1], [], [])
flow = crn.flow(isLNA, derivatives)
return flow, iSATParser.constructISAT(crn,
specification,
flow,
costFunction='')
def exampleCRN():
A = Species('A')
B = Species('B')
x1 = Species('x_1')
x2 = Species('x_2')
reaction1 = Reaction([Term(A, 1), Term(x1, 1)],
[Term(x1, 1), Term(x1, 1)], RateConstant('k_1', 1, 2))
reaction2 = Reaction([Term(x1, 1), Term(x2, 1)], [Term(x2, 2)],
RateConstant('k_2', 1, 2))
reaction3 = Reaction([Term(x2, 1)], [Term(B, 1)],
RateConstant('k_3', 1, 2))
crn = CRNSketch([reaction1, reaction2, reaction3], [], [])
isLNA = False
derivatives = []
specification = []
flow = crn.flow(isLNA, derivatives)
return iSATParser.constructISAT(crn, specification, flow, costFunction='')
def synthesize_with_isat(crn):
derivatives = []
flow = crn.flow(True, derivatives)
# specification_dreal = [('','cA > A','')]
specification = [('', '', '')]
flow = crn.flow(False, derivatives)
hys = iSATParser.constructISAT(crn, specification, flow, max_time=100)
with open('superpoisson.hys', 'w') as file:
file.write(hys)
sc = SolverCallerISAT(
"./superpoisson.hys",
isat_path="../isat-ode-r2806-static-x86_64-generic-noSSE-stripped.txt")
result_files = sc.single_synthesis(cost=0, precision=0.01, msw=0.05)
# result_files = ["./results/sixreactionstar_0_0.01-isat.txt"]
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 + "-simulation.png",
t=linspace(0, 100, 1000))
print("\n\n")
print(variable_names)
print(sol)
savetxt(file_name + "-simulation.csv", sol, delimiter=",")
def hill_function_example():
X = Species('X')
Y = Species('Y')
vmax = RateConstant('V_max', 0.1, 10)
km = RateConstant('Km', 0.1, 10)
n = RateConstant('n', 0.1, 10)
#reaction = HillReaction([(X, 2)], [(Y,3)], vmax, km, n)
#reaction = HillReaction([ TermChoice(0, [(X, 2), (Y, 2)])], [(Y,4)], vmax, km, n)
reaction = HillReaction(
[TermChoice(0, [(LambdaChoice([X, Y], 1), 2),
(Y, 4)])], [(Y, 5)], vmax, km, n)
reaction = HillReaction([(LambdaChoice([X, Y], 1), 2), (Y, 4)], [(Y, 5)],
vmax, km, n)
derivatives = []
crn = CRNSketch([reaction], [], [])
flow = crn.flow(False, derivatives)
crn.get_cost()
return iSATParser.constructISAT(crn, [], flow, costFunction='')
