def simulate_toy(sbml_path, out_dir, dts=[0.1, 1.0, 5.0], figures=True, tend=50, ode_integrator="cvode"):
""" Simulate the diauxic growth model.
:return: solution data frame
"""
plot_kwargs = {
'markersize': 4,
'marker': 's',
'alpha': 0.5
}
dfs = []
for dt in dts:
df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=tend, dt=dt, ode_integrator=ode_integrator)
dfs.append(df)
analyse_uniqueness(dfba_simulator)
# generic analysis
analysis = DFBAAnalysis(df=df, ode_model=dfba_simulator.ode_model)
if figures:
analysis.plot_reactions(os.path.join(out_dir, "fig_reactions_generic_dt{}.png".format(dt)),
**plot_kwargs)
analysis.plot_species(os.path.join(out_dir, "fig_species_generic_dt{}.png".format(dt)),
**plot_kwargs)
analysis.save_csv(os.path.join(out_dir, "data_simulation_generic_dt{}.csv".format(dt)))
# custom model plots
if figures:
print_species(dfs=dfs, filepath=os.path.join(out_dir, "fig_species.png"), **plot_kwargs)
print_fluxes(dfs=dfs, filepath=os.path.join(out_dir, "fig_fluxes.png"), **plot_kwargs)
return dfs
def simulate_diauxic_growth(sbml_path, out_dir, dts=[0.01, 0.1], figures=True):
""" Simulate the diauxic growth model.
:return: solution data frame
"""
tend = 15
dfs = []
for dt in dts:
df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=tend, dt=dt, pfba=False)
dfs.append(df)
# uniqueness of solution
analyse_uniqueness(dfba_simulator)
# generic analysis
# analysis = DFBAAnalysis(df=df, rr_comp=dfba_simulator.ode_model)
# analysis.plot_reactions(os.path.join(out_dir, "fig_reactions_generic_dt{}.png".format(dt)),
# **plot_kwargs)
# analysis.plot_species(os.path.join(out_dir, "fig_species_generic_dt{}.png".format(dt)),
# **plot_kwargs)
# analysis.save_csv(os.path.join(out_dir, "data_simulation_generic_dt{}.csv".format(dt)))
if figures:
# custom model plots
plot_kwargs = {
'markersize': 4,
'marker': 'None',
'alpha': 0.5
}
analyse.print_species(filepath=os.path.join(out_dir, "fig_species.png"), dfs=dfs, **plot_kwargs)
analyse.print_fluxes(filepath=os.path.join(out_dir, "fig_fluxes.png"), dfs=dfs, **plot_kwargs)
return dfs
def simulate_toy(sbml_path,
out_dir,
dts=[0.1, 1.0, 5.0],
figures=True,
tend=50,
ode_integrator="cvode"):
""" Simulate the diauxic growth model.
:return: solution data frame
"""
plot_kwargs = {'markersize': 4, 'marker': 's', 'alpha': 0.5}
dfs = []
for dt in dts:
df, dfba_model, dfba_simulator = simulate_dfba(
sbml_path, tend=tend, dt=dt, ode_integrator=ode_integrator)
dfs.append(df)
analyse_uniqueness(dfba_simulator)
# generic analysis
analysis = DFBAAnalysis(df=df, ode_model=dfba_simulator.ode_model)
if figures:
analysis.plot_reactions(
os.path.join(out_dir,
"fig_reactions_generic_dt{}.png".format(dt)),
**plot_kwargs)
analysis.plot_species(
os.path.join(out_dir,
"fig_species_generic_dt{}.png".format(dt)),
**plot_kwargs)
analysis.save_csv(
os.path.join(out_dir,
"data_simulation_generic_dt{}.csv".format(dt)))
# custom model plots
if figures:
print_species(dfs=dfs,
filepath=os.path.join(out_dir, "fig_species.png"),
**plot_kwargs)
print_fluxes(dfs=dfs,
filepath=os.path.join(out_dir, "fig_fluxes.png"),
**plot_kwargs)
return dfs
# In[3]:
# get the absolute path to the top model
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
sbml_path = os.path.join(
utils.versioned_directory(toysettings.OUT_DIR, toysettings.VERSION),
toysettings.TOP_LOCATION)
print(sbml_path)
# run simulation with the top model
from sbmlutils.dfba.simulator import simulate_dfba
df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=50, dt=5.0)
df
# ## Toy example
# In[4]:
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
import tempfile
test_dir = tempfile.mkdtemp()
# create the toy model
toyfactory.create_model(test_dir)
# In[3]:
# get the absolute path to the top model
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
sbml_path = os.path.join(utils.versioned_directory(toysettings.OUT_DIR, toysettings.VERSION),
toysettings.TOP_LOCATION)
print(sbml_path)
# run simulation with the top model
from sbmlutils.dfba.simulator import simulate_dfba
df, dfba_model, dfba_simulator = simulate_dfba(sbml_path, tend=50, dt=5.0)
df
# ## Toy example
# In[4]:
from sbmlutils.dfba.toy_wholecell import settings as toysettings
from sbmlutils.dfba.toy_wholecell import model_factory as toyfactory
from sbmlutils.dfba.toy_wholecell import simulate as toysimulate
import tempfile
test_dir = tempfile.mkdtemp()