def bounds_model(sbml_file, directory, doc_fba=None): """" Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model. """ doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) # dt compartment_id = "blood" builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=True) # compartment builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # dynamic species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=True) # bounds builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) # bounds fba_prefix = "fba" model_fba = doc_fba.getModel() objects = [] ex_rids = utils.find_exchange_reactions(model_fba) for ex_rid, sid in ex_rids.items(): r = model_fba.getReaction(ex_rid) # lower & upper bound parameters r_fbc = r.getPlugin(builder.SBML_FBC_NAME) lb_id = r_fbc.getLowerFluxBound() fba_lb_id = fba_prefix + lb_id lb_value = model_fba.getParameter(lb_id).getValue() objects.extend([ # default bounds from fba mc.Parameter(sid=fba_lb_id, value=lb_value, unit=UNIT_FLUX, constant=False), # uptake bounds (lower bound) mc.AssignmentRule(sid=lb_id, value="max({}, -{}*{}/dt)".format(fba_lb_id, compartment_id, sid)), ]) mc.create_objects(model, objects) sbmlio.write_sbml(doc, filepath=pjoin(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba=None): """" Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model. """ doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) # dt compartment_id = "blood" builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=True) # compartment builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # dynamic species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=True) # bounds builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) # bounds fba_prefix = "fba" model_fba = doc_fba.getModel() objects = [] ex_rids = utils.find_exchange_reactions(model_fba) for ex_rid, sid in ex_rids.items(): r = model_fba.getReaction(ex_rid) # lower & upper bound parameters r_fbc = r.getPlugin(builder.SBML_FBC_NAME) lb_id = r_fbc.getLowerFluxBound() fba_lb_id = fba_prefix + lb_id lb_value = model_fba.getParameter(lb_id).getValue() objects.extend([ # default bounds from fba mc.Parameter(sid=fba_lb_id, value=lb_value, unit=UNIT_FLUX, constant=False), # uptake bounds (lower bound) mc.AssignmentRule(sid=lb_id, value="max({}, -{}*{}/dt)".format(fba_lb_id, compartment_id, sid)), ]) mc.create_objects(model, objects) sbmlio.write_sbml(doc, filepath=pjoin(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba, annotations=None): """" Bounds model. """ bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=True) # compartment compartment_id = 'extern' builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, hasOnlySubstanceUnits=True, create_port=True) # exchange bounds builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) objects = [ # exchange bounds # FIXME: readout the FBA network bounds mc.Parameter(sid="lb_default", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True), # kinetic bound parameter & calculation mc.Parameter(sid='ub_R1', value=1.0, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000625"), mc.Parameter(sid='k1', value=-0.2, unit="per_s", name="k1", constant=False), mc.RateRule(sid="ub_R1", value="k1*ub_R1"), # bound assignment rules mc.AssignmentRule(sid="lb_EX_A", value='max(lb_default, -A/dt)'), mc.AssignmentRule(sid="lb_EX_C", value='max(lb_default, -C/dt)'), ] mc.create_objects(model, objects) # ports comp.create_ports(model, portType=comp.PORT_TYPE_PORT, idRefs=["ub_R1"]) if annotations: annotation.annotate_sbml_doc(doc, annotations) sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba, annotations=None): """" Bounds model. """ bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=True) # compartment compartment_id = 'extern' builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, hasOnlySubstanceUnits=True, create_port=True) # exchange bounds builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) objects = [ # exchange bounds # FIXME: readout the FBA network bounds mc.Parameter(sid="lb_default", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=True), # kinetic bound parameter & calculation mc.Parameter(sid='ub_R1', value=1.0, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000625"), mc.Parameter(sid='k1', value=-0.2, unit="per_s", name="k1", constant=False), mc.RateRule(sid="ub_R1", value="k1*ub_R1"), # bound assignment rules mc.AssignmentRule(sid="lb_EX_A", value='max(lb_default, -A/dt)'), mc.AssignmentRule(sid="lb_EX_C", value='max(lb_default, -C/dt)'), ] mc.create_objects(model, objects) # ports comp.create_ports(model, portType=comp.PORT_TYPE_PORT, idRefs=["ub_R1"]) if annotations: annotator.annotate_sbml_doc(doc, annotations) sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba, annotations=None): """" Bounds model. """ bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=True) # compartment compartment_id = 'cell' builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, hasOnlySubstanceUnits=False, create_port=True) # exchange bounds builder.create_exchange_bounds(model_bounds=model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) builder.create_dynamic_bounds(model_bounds=model, model_fba=model_fba, unit_flux=UNIT_FLUX) # annotations if annotations: annotator.annotate_sbml_doc(doc, annotations) sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba=None): """" Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model. The units of the exchange fluxes must fit to the transported species. """ doc = builder.template_doc_bounds("ecoli") model = doc.getModel() bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) # dt compartment_id = "bioreactor" builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=True) # compartment builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # dynamic species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=True, exclude_sids=['X']) # FIXME: define biomass separately, also port needed for biomass mc.create_objects(model, [ mc.Parameter(sid='cf_X', value=1.0, unit="g_per_mmol", name="biomass conversion factor", constant=True), mc.Species(sid='X', initialAmount=0.001, compartment=compartment_id, name='biomass', substanceUnit='g', hasOnlySubstanceUnits=True, conversionFactor='cf_X') ]) # exchange & dynamic bounds if not biomass_weighting: builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) builder.create_dynamic_bounds(model, model_fba, unit_flux=UNIT_FLUX) else: builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX_PER_G, create_ports=True) builder.create_dynamic_bounds(model, model_fba, unit_flux=UNIT_FLUX_PER_G) sbmlio.write_sbml(doc, filepath=pjoin(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba, annotations=None): """" Bounds model. """ bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) builder.create_dfba_dt(model, step_size=DT_SIM, time_unit=UNIT_TIME, create_port=True) # compartment compartment_id = 'cell' builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, hasOnlySubstanceUnits=False, create_port=True) # exchange bounds builder.create_exchange_bounds(model_bounds=model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) builder.create_dynamic_bounds(model_bounds=model, model_fba=model_fba, unit_flux=UNIT_FLUX) # annotations if annotations: annotation.annotate_sbml_doc(doc, annotations) sbmlio.write_sbml(doc, filepath=os.path.join(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba=None, annotations=None): """" Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model. """ # TODO: the bounds model should be created based on the FBA model (i.e. use the exchange reactions # to create the bounds info. bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) # dt compartment_id = "bioreactor" builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=True) # compartment builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # dynamic species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=True) # bounds builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) # bounds fba_infix = "fba_" model_fba = doc_fba.getModel() objects = [] ex_rids = utils.find_exchange_reactions(model_fba) for ex_rid, sid in ex_rids.items(): r = model_fba.getReaction(ex_rid) # lower & upper bound parameters r_fbc = r.getPlugin(builder.SBML_FBC_NAME) lb_id = r_fbc.getLowerFluxBound() fba_lb_id = builder.LOWER_BOUND_PREFIX + fba_infix + ex_rid lb_value = model_fba.getParameter(lb_id).getValue() objects.extend([ # default bounds from fba mc.Parameter(sid=fba_lb_id, value=lb_value, unit=UNIT_FLUX, constant=False), ]) mc.create_objects(model, objects) objects = [ # kinetic lower bounds mc.Parameter(sid="lb_kin_EX_Glcxt", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000612"), mc.Parameter(sid="lb_kin_EX_O2", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000612"), # parameters for kinetic bounds mc.Parameter(sid='Vmax_EX_O2', value=15, unit=UNIT_FLUX, constant=True), mc.Parameter(sid='Vmax_EX_Glcxt', value=10, unit=UNIT_FLUX, constant=True), mc.Parameter(sid='Km_EX_Glcxt', value=0.015, unit=UNIT_CONCENTRATION, name="Km_vGlcxt", constant=True), # kinetic bounds (unintuitive direction due to the identical concentrations in bioreactor and model) mc.AssignmentRule(sid="lb_kin_EX_Glcxt", value="-Vmax_EX_Glcxt * Glcxt/(Km_EX_Glcxt + Glcxt)"), mc.AssignmentRule(sid="lb_kin_EX_O2", value="-Vmax_EX_O2"), # exchange reaction bounds # uptake bounds (lower bound) # TODO: FIXME the X hack # the bounds for the fba model have to be in mmol/h/gdw mc.AssignmentRule(sid="lb_EX_Ac", value="max(lb_fba_EX_Ac, -Ac/X/1 l_per_mmol*bioreactor/dt)"), mc.AssignmentRule(sid="lb_EX_X", value="max(lb_fba_EX_X, -X/X/1 l_per_mmol*bioreactor/dt)"), mc.AssignmentRule(sid="lb_EX_Glcxt", value="max(lb_kin_EX_Glcxt, -Glcxt/X/1 l_per_mmol*bioreactor/dt)"), mc.AssignmentRule(sid="lb_EX_O2", value="max(lb_kin_EX_O2, -O2/X/1 l_per_mmol*bioreactor/dt)"), ] mc.create_objects(model, objects) if annotations: annotation.annotate_sbml_doc(doc, annotations) sbmlio.write_sbml(doc, filepath=pjoin(directory, sbml_file), validate=True)
def bounds_model(sbml_file, directory, doc_fba=None, annotations=None): """" Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model. """ # TODO: the bounds model should be created based on the FBA model (i.e. use the exchange reactions # to create the bounds info. bounds_notes = notes.format(""" <h2>BOUNDS submodel</h2> <p>Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.</p> """) doc = builder.template_doc_bounds(settings.MODEL_ID) model = doc.getModel() utils.set_model_info(model, notes=bounds_notes, creators=creators, units=units, main_units=main_units) # dt compartment_id = "bioreactor" builder.create_dfba_dt(model, time_unit=UNIT_TIME, create_port=True) # compartment builder.create_dfba_compartment(model, compartment_id=compartment_id, unit_volume=UNIT_VOLUME, create_port=True) # dynamic species model_fba = doc_fba.getModel() builder.create_dfba_species(model, model_fba, compartment_id=compartment_id, unit_amount=UNIT_AMOUNT, create_port=True) # bounds builder.create_exchange_bounds(model, model_fba=model_fba, unit_flux=UNIT_FLUX, create_ports=True) # bounds fba_infix = "fba_" model_fba = doc_fba.getModel() objects = [] ex_rids = utils.find_exchange_reactions(model_fba) for ex_rid, sid in ex_rids.items(): r = model_fba.getReaction(ex_rid) # lower & upper bound parameters r_fbc = r.getPlugin(builder.SBML_FBC_NAME) lb_id = r_fbc.getLowerFluxBound() fba_lb_id = builder.LOWER_BOUND_PREFIX + fba_infix + ex_rid lb_value = model_fba.getParameter(lb_id).getValue() objects.extend([ # default bounds from fba Parameter(sid=fba_lb_id, value=lb_value, unit=UNIT_FLUX, constant=False), ]) factory.create_objects(model, objects) objects = [ # kinetic lower bounds Parameter(sid="lb_kin_EX_Glcxt", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000612"), Parameter(sid="lb_kin_EX_O2", value=builder.LOWER_BOUND_DEFAULT, unit=UNIT_FLUX, constant=False, sboTerm="SBO:0000612"), # parameters for kinetic bounds Parameter(sid='Vmax_EX_O2', value=15, unit=UNIT_FLUX, constant=True), Parameter(sid='Vmax_EX_Glcxt', value=10, unit=UNIT_FLUX, constant=True), Parameter(sid='Km_EX_Glcxt', value=0.015, unit=UNIT_CONCENTRATION, name="Km_vGlcxt", constant=True), # kinetic bounds (unintuitive direction due to the identical concentrations in bioreactor and model) AssignmentRule(sid="lb_kin_EX_Glcxt", value="-Vmax_EX_Glcxt * Glcxt/(Km_EX_Glcxt + Glcxt)"), AssignmentRule(sid="lb_kin_EX_O2", value="-Vmax_EX_O2"), # exchange reaction bounds # uptake bounds (lower bound) # TODO: FIXME the X hack # the bounds for the fba model have to be in mmol/h/gdw AssignmentRule( sid="lb_EX_Ac", value="max(lb_fba_EX_Ac, -Ac/X/1 l_per_mmol*bioreactor/dt)"), AssignmentRule( sid="lb_EX_X", value="max(lb_fba_EX_X, -X/X/1 l_per_mmol*bioreactor/dt)"), AssignmentRule( sid="lb_EX_Glcxt", value="max(lb_kin_EX_Glcxt, -Glcxt/X/1 l_per_mmol*bioreactor/dt)"), AssignmentRule( sid="lb_EX_O2", value="max(lb_kin_EX_O2, -O2/X/1 l_per_mmol*bioreactor/dt)"), ] factory.create_objects(model, objects) if annotations: annotator.annotate_sbml_doc(doc, annotations) sbmlio.write_sbml(doc, filepath=pjoin(directory, sbml_file), validate=True)