def __display_pathways_information(predicted_pathways, host, original_model):
# TODO: remove copy hack.
with Grid(nrows=2, title="Production envelopes for %s (%s)" % (host.name, original_model.id)) as grid:
for i, pathway in enumerate(predicted_pathways):
pathway_id = "Pathway %i" % (i + 1)
with TimeMachine() as tm:
pathway.plug_model(original_model, tm)
production_envelope = phenotypic_phase_plane(original_model,
variables=[original_model.biomass],
objective=pathway.product)
production_envelope.plot(grid, title=pathway_id, width=400, height=300)
def production_envelope(self, model, objective=None):
with model:
self.apply(model)
return phenotypic_phase_plane(model, variables=[objective], objective=self.product.id)
def production_envelope(self, model, objective=None):
with model:
self.apply(model)
return phenotypic_phase_plane(model,
variables=[objective],
objective=self.product.id)
def production_envelope(self, model, objective=None):
with TimeMachine() as tm:
self.plug_model(model, tm)
return phenotypic_phase_plane(model,
variables=[objective],
objective=self.product)
''' Created on 16 Nov 2017 @author: mate ''' from cameo import models # models.bigg.e_coli_core.solve() model = models.bigg.iJO1366 # wt_solution = model.solve() # model.solve() does not work, but model.optimize() does wt_solution = model.optimize() growth = wt_solution.fluxes["BIOMASS_Ec_iJO1366_core_53p95M"] acetate_production = wt_solution.fluxes["EX_ac_e"] from cameo import phenotypic_phase_plane p = phenotypic_phase_plane(model, variables=['BIOMASS_Ec_iJO1366_core_53p95M'], objective='EX_ac_e') p.plot(points=[(growth, acetate_production)])
def production_envelope(self, model, objective=None):
with TimeMachine() as tm:
self.plug_model(model, tm)
return phenotypic_phase_plane(model, variables=[objective], objective=self.product)