def medium_Lactate_optim(isMultiProc=False, size=1, withCobraPy=False):
SBML_FILE = "../../../examples/models/Ec_iAF1260.xml"
modelaux = load_cbmodel(SBML_FILE, flavor="cobra")
model = fix_exchange_reactions_model(modelaux)
fileRes = basePath + "Results/optim_Ec_iAF1260_medium_lactate.csv"
simulProb = StoicSimulationProblem(
model,
objective={"R_Ec_biomass_iAF1260_core_59p81M": 1},
withCobraPy=withCobraPy)
fba = simulProb.simulate()
# calculate the essential uptake reactions to biomass production
essential = simulProb.find_essential_drains()
print(essential)
if simulProb.constraints:
simulProb.constraints.update(
{reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential}) # put essential reactions as constraints
else:
simulProb.constraints = {
reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential
}
criticalReacs = essential
# set the minimum production of biomass
simulProb.set_objective_function({"R_EX_lac_L_e": 1})
simulProb.constraints.update({
"R_Ec_biomass_iAF1260_core_59p81M":
(fba.get_fluxes_distribution()["R_Ec_biomass_iAF1260_core_59p81M"] *
0.75, 9999)
})
minObjective = {"R_EX_lac_L_e": 1e-5}
print(
"Biomass: " +
str(fba.get_fluxes_distribution()["R_Ec_biomass_iAF1260_core_59p81M"] *
0.75))
build_evaluation_function
evalFunc = build_evaluation_function("MinNumberReac", size, minObjective)
cbm_strain_optim(simulProb,
evaluationFunc=evalFunc,
levels=None,
type=optimType.MEDIUM,
criticalReacs=criticalReacs,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes)
def framed_optim(isMultiProc, size):
model = load_cbmodel(SBML_FILE, flavor="cobra")
fileRes = basePath + "Results/optim_Ec_iAF1260_ko.csv"
simulProb = StoicSimulationProblem(
model, objective={"R_Ec_biomass_iAF1260_core_59p81M": 1})
objFunc = build_evaluation_function("targetFlux",
["R_Ec_biomass_iAF1260_core_59p81M"])
cbm_strain_optim(simulProb,
evaluationFunc=objFunc,
levels=None,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes)
def medium_SC_Etanol_Levels_optim(isMultiProc=False,
size=1,
withCobraPy=False):
SBML_FILE = "../../../examples/models/iMM904.xml"
model = load_cbmodel(SBML_FILE, flavor="fbc2")
fileRes = basePath + "Results/optim_iMM904_etanol_levels.csv"
simulProb = StoicSimulationProblem(model,
objective={"R_BIOMASS_SC5_notrace": 1},
withCobraPy=withCobraPy)
fba = simulProb.simulate()
print("Biomass: " +
str(fba.get_fluxes_distribution()["R_BIOMASS_SC5_notrace"]))
# calculate the essential uptake reactions to biomass production
essential = simulProb.find_essential_drains()
print(essential)
if simulProb.constraints:
simulProb.constraints.update(
{reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential}) # put essential reactions as constraints
else:
simulProb.constraints = {
reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential
}
criticalReacs = essential
# set the minimum production of biomass
simulProb.set_objective_function({"R_EX_etoh_e": 1})
simulProb.constraints.update({
"R_BIOMASS_SC5_notrace":
(fba.get_fluxes_distribution()["R_BIOMASS_SC5_notrace"] * 0.75, 9999)
})
print("Biomass: " +
str(fba.get_fluxes_distribution()["R_BIOMASS_SC5_notrace"] * 0.75))
evalFunc = build_evaluation_function(
"MinNumberReacAndMaxFluxWithLevels", size, LEVELS,
{"R_EX_etoh_e": model.reactions["R_EX_etoh_e"].ub})
cbm_strain_optim(simulProb,
evaluationFunc=evalFunc,
levels=LEVELS,
type=optimType.MEDIUM_LEVELS,
criticalReacs=criticalReacs,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes)
def medium_reac_ko_optim(isMultiProc=False, size=[5, 5], withCobraPy=False):
SBML_FILE = "../../../examples/models/Ec_iAF1260.xml"
model = load_cbmodel(SBML_FILE, flavor="cobra")
newModel = fix_exchange_reactions_model(model)
fileRes = basePath + "Results/optim_Ec_iAF1260_medium_ko_succ.csv"
simulProb = StoicSimulationProblem(
newModel,
objective={"R_Ec_biomass_iAF1260_core_59p81M": 1},
withCobraPy=withCobraPy)
# set the minimum production of biomass
fba = simulProb.simulate()
# calculate the essential uptake reactions to biomass production
essential = simulProb.find_essential_drains()
print(essential)
if simulProb.constraints:
simulProb.constraints.update(
{reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential}) # put essential reactions as constraints
else:
simulProb.constraints = {
reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential
}
simulProb.set_objective_function({"R_EX_succ_e_": 1})
simulProb.constraints.update({
"R_Ec_biomass_iAF1260_core_59p81M":
(fba.get_fluxes_distribution()["R_Ec_biomass_iAF1260_core_59p81M"] *
0.25, 9999)
})
print(
"Biomass: " +
str(fba.get_fluxes_distribution()["R_Ec_biomass_iAF1260_core_59p81M"] *
0.25))
evalFunc = build_evaluation_function(
"MinNumberReacAndMaxFlux", sum(size),
{"R_EX_succ_e": model.reactions["R_EX_succ_e"].ub})
cbm_strain_optim(simulProb,
evaluationFunc=evalFunc,
levels=None,
type=optimType.MEDIUM_REACTION_KO,
criticalReacs=essential,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes) # KO_Reaction by default
def reac_ko_medium_optim_CM(isMultiProc=False, size=(1, 1), withCobraPy=False):
SBML_FILE = basePath + "Data/EC_SC_model.xml"
modelaux = load_cbmodel(SBML_FILE, exchange_detection_mode="R_EX_")
model = fix_exchange_reactions_model(modelaux)
fileRes = basePath + "Results/optim_Comunity_KO_medium_pFBA.csv"
for r_id, rxn in model.reactions.items():
if r_id.startswith(
'R_EX_'): # ou tambem podes fazer if rxn.is_exchange:
rxn.lb = -1000 if rxn.lb is None else rxn.lb
rxn.ub = 1000 if rxn.ub is None else rxn.ub
simulProb = StoicSimulationProblem(model,
objective={"R_BM_total_Synth": 1},
withCobraPy=withCobraPy)
res = simulProb.simulate()
print(res.print())
evalFunc = build_evaluation_function("BP_MinModifications",
"R_BM_total_Synth",
"R_EX_succ_medium_")
result = cbm_strain_optim(simulProb,
evaluationFunc=evalFunc,
levels=None,
type=optimType.MEDIUM_REACTION_KO,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes)
def cobra_optim(isMultiProc, size):
model = read_sbml_model(SBML_FILE)
fileRes = basePath + "Results/optim_Ec_iAF1260_ko_cobra.csv"
simulProb = StoicSimulationProblem(
model,
objective={"Ec_biomass_iAF1260_core_59p81M": 1},
withCobraPy=True)
objFunc = build_evaluation_function("targetFlux",
["Ec_biomass_iAF1260_core_59p81M"])
print(simulProb.simulate())
cbm_strain_optim(simulProb,
evaluationFunc=objFunc,
levels=None,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes)
def medium_SC_optim(isMultiProc=False, size=1, withCobraPy=False):
SBML_FILE = "../../../examples/models/iMM904.xml"
model = load_cbmodel(SBML_FILE, flavor="fbc2")
fileRes = basePath + "Results/optim_iMM904_medium.csv"
simulProb = StoicSimulationProblem(model,
objective={"R_BIOMASS_SC5_notrace": 1},
withCobraPy=withCobraPy)
fba = simulProb.simulate()
# calculate the essential uptake reactions to biomass production
essential = simulProb.find_essential_drains()
print(essential)
if simulProb.constraints:
simulProb.constraints.update(
{reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential}) # put essential reactions as constraints
else:
simulProb.constraints = {
reac: (StoicConfigurations.DEFAULT_LB, 0)
for reac in essential
}
criticalReacs = essential
# set the minimum production of biomass
minObjective = {
"R_BIOMASS_SC5_notrace":
fba.get_fluxes_distribution()["R_BIOMASS_SC5_notrace"] * 0.75
}
evalFunc = build_evaluation_function("MinNumberReac", size, minObjective)
cbm_strain_optim(simulProb,
evaluationFunc=evalFunc,
levels=None,
type=optimType.MEDIUM,
criticalReacs=criticalReacs,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes)
def stoic_optimization(model, optim_type, eval_func, **kwargs):
cand_size = kwargs.get("size", None)
stoic_obj = kwargs.get("objective", {})
withCobraPy = cobra_or_framed(model)
min_flag = kwargs.get("minimize", False)
multi_thread = kwargs.get("isMultiProc", False)
stoic_constraints = kwargs.get("constraints", {})
output_file = kwargs.get("output_file", "results.csv")
stoic_method = kwargs.get("method", StoicConfigurations.SOLVER_METHOD)
stoic_uo_levels = kwargs.get(
"levels",
[2**-5, 2**-4, 2**-3, 2**-2, 2**-1, 2**1, 2**2, 2**3, 2**4, 2**5])
types_dict = {
"KO": optimType.REACTION_KO,
"UO": optimType.REACTION_UO,
"MEDKO": optimType.MEDIUM,
"MEDUO": optimType.MEDIUM_LEVELS,
"KO+MEDKO": optimType.MEDIUM_REACTION_KO
}
stoic_simul_problem = StoicSimulationProblem(model=model,
objective=stoic_obj,
minimize=min_flag,
constraints=stoic_constraints,
method=stoic_method,
withCobraPy=withCobraPy)
critical_proteins = kwargs.get("critical_proteins", [])
if critical_proteins == "auto":
critical_proteins = stoic_simul_problem.find_essential_drains()
res = cbm_strain_optim(simulProblem=stoic_simul_problem,
evaluationFunc=eval_func,
levels=stoic_uo_levels,
type=types_dict[optim_type],
criticalReacs=critical_proteins,
isMultiProc=multi_thread,
candidateSize=cand_size,
resultFile=output_file)
return res
def reac_ko_optim(isMultiProc=False, size=1, withCobraPy=False):
SBML_FILE = "../../../examples/models/Ec_iAF1260.xml"
if withCobraPy:
model = read_sbml_model(SBML_FILE)
fileRes = basePath + "Results/optim_Ec_iAF1260_ko_cobra.csv"
else:
model = load_cbmodel(SBML_FILE, flavor="cobra")
fileRes = basePath + "Results/optim_Ec_iAF1260_ko.csv"
simulProb = StoicSimulationProblem(
model,
objective={"Ec_biomass_iAF1260_core_59p81M": 1},
withCobraPy=withCobraPy)
evalFunc = build_evaluation_function("targetFlux",
["Ec_biomass_iAF1260_core_59p81M"])
result = cbm_strain_optim(simulProb,
evaluationFunc=evalFunc,
levels=None,
isMultiProc=isMultiProc,
candidateSize=size,
resultFile=fileRes) # KO_Reaction by default
result.print()