import copy from cameo import load_model from cameo.methods import DifferentialFVA from cameo.basics import production_envelope model = load_model('../tests/data/EcoliCore.xml') solution = model.optimize() surrogate_experimental_fluxes = dict([(key, (val * .8, val * 1.2)) for key, val in solution.x_dict.iteritems()]) constraint_model = copy.copy(model) for reaction_id, (lb, ub) in surrogate_experimental_fluxes.iteritems(): reaction = constraint_model.reactions.get_by_id(reaction_id) reaction.lower_bound = lb reaction.upper_bound = ub diffFVA = DifferentialFVA(design_space_model=model, reference_model=constraint_model, target='EX_succ_LPAREN_e_RPAREN_', variables=[model.reactions.Biomass_Ecoli_core_N_LPAREN_w_FSLASH_GAM_RPAREN__Nmet2]) print diffFVA.run()
from multiprocessing import Pool model = load_model('../tests/data/iJO1366.pickle') reference_model = copy(model) reference_model.reactions.get_by_id('Ec_biomass_iJO1366_core_53p95M').lower_bound = 0.9823718127270133 # t1 = time.time() # fva_solution = flux_variability_analysis(model) # t2 = time.time() # print "Execution time: %s" % (t2-t1) # t1 = time.time() # fva_solution = flux_variability_analysis(model, view=ViewFacade()) # t2 = time.time() # print "Execution time: %s" % (t2-t1) # t1 = time.time() # fva_solution = flux_variability_analysis(model, ) # t2 = time.time() # print "Execution time: %s" % (t2-t1) dFVA = DifferentialFVA(design_space_model=model, reference_model=reference_model, target='EX_succ_e', variables=['Ec_biomass_iJO1366_core_53p95M'] ) dFVA.run()