# Sabaody # Copyright 2018 J Kyle Medley from __future__ import print_function, division, absolute_import from roadrunner import RoadRunner, Logger Logger.disableConsoleLogging() Logger.setLevel(Logger.LOG_FATAL) from params import getDefaultParamValues, getUpperBound, getLowerBound from b2problem import B2_UDP from pygmo import island as pg_island, problem, rosenbrock, simulated_annealing, de, mp_island from math import sqrt def benchmark_loading_time(): import arrow time_start = arrow.utcnow() r = RoadRunner('../../../../../sbml/b2.xml') delta_t = arrow.utcnow() - time_start print('Loading time:', delta_t) def benchmark_simulated_annealing(): island = pg_island( algo=simulated_annealing(Ts=1.,Tf=.01), prob=problem(B2_UDP(getLowerBound(),getUpperBound(),'../../../../../sbml/b2.xml')), size=10) N = 10 import arrow time_start = arrow.utcnow()
from roadrunner import RoadRunner, Logger #Logger.setLevel(Logger.LOG_DEBUG) # too verbose Logger.setLevel(Logger.LOG_WARNING) # Load model rr = RoadRunner('/tmp/tx.sbml') #rr = RoadRunner('/tmp/tx-reduced.sbml') #rr = RoadRunner('/tmp/antsbml.xml') # Simulate model results = rr.simulate(0, 10, 30, integrator='gillespie') print(results) # Write results to temp file with open('/tmp/sim_res.csv', 'w') as f: f.write(str(results)) # Plot rr.plot()