In [3]:

    

from cameo import models, phenotypic_phase_plane


    

In [63]:

    

model = models.bigg.e_coli_core.copy()


    

In [64]:

    

model.reactions.EX_o2_e.lower_bound = 0


    

In [24]:

    

model.reactions.EX_succ_e


    

    
Out[24]:





        

            

                
Id
EX_succ_e
            
            

                
Name
Succinate exchange
            
            

                
Stoichiometry
succ_e --> 
            
            

                
Lower bound
0.000000
            
            

                
Upper bound
1000.000000
            
        
        

In [25]:

    

ppp = phenotypic_phase_plane(model,
                             variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=model.reactions.EX_succ_e)

ppp.plot()


    

In [39]:

    

mutant1 = model.copy()


    

In [40]:

    

mutant1.reactions.ACKr.knock_out()
mutant1.reactions.ATPS4r.knock_out()
mutant1.reactions.ATPM.knock_out()
mutant1.reactions.FUM.knock_out()


    

In [41]:

    

ppp = phenotypic_phase_plane(mutant1,
                             variables=[mutant1.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant1.reactions.EX_succ_e)

ppp.plot()


    

In [33]:

    

mutant2 = model.copy()


    

In [35]:

    

mutant2.reactions.ACALD.knock_out()
mutant2.reactions.PYK.knock_out()
mutant2.reactions.ME2.knock_out()


    

In [36]:

    

ppp = phenotypic_phase_plane(mutant2,
                             variables=[mutant2.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant2.reactions.EX_succ_e)

ppp.plot()


    

In [42]:

    

mutant3 = model.copy()


    

In [43]:

    

mutant3.reactions.ACALD.knock_out()
mutant3.reactions.LDH_D.knock_out()


    

In [44]:

    

ppp = phenotypic_phase_plane(mutant3,
                             variables=[mutant3.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant3.reactions.EX_succ_e)

ppp.plot()


    

In [67]:

    

### Solution 1


    

In [46]:

    

mutant1.reactions.EX_o2_e.lower_bound = -20
ppp = phenotypic_phase_plane(mutant1,
                             variables=[mutant1.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant1.reactions.EX_succ_e)

ppp.plot()


    

In [47]:

    

mutant2.reactions.EX_o2_e.lower_bound = -20
ppp = phenotypic_phase_plane(mutant2,
                             variables=[mutant2.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant2.reactions.EX_succ_e)

ppp.plot()


    

In [49]:

    

mutant3.reactions.EX_o2_e.lower_bound = -20
ppp = phenotypic_phase_plane(mutant3,
                             variables=[mutant3.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant3.reactions.EX_succ_e)

ppp.plot()


    

In [53]:

    

mutant3.reactions.ACALD.gene_name_reaction_rule


    

    
Out[53]:





'mhpF or adhE'

In [54]:

    

mutant3.reactions.LDH_D.gene_name_reaction_rule


    

    
Out[54]:





'dld or ldhA'

In [58]:

    

for gene in mutant3.reactions.ACALD.genes:
    print(gene.name, gene.reactions)


    

    




adhE frozenset({<Reaction ALCD2x at 0x7f8f21a0e908>, <Reaction ACALD at 0x7f8f21a0e668>})
mhpF frozenset({<Reaction ACALD at 0x7f8f21a0e668>})

In [59]:

    

for gene in mutant3.reactions.LDH_D.genes:
    print(gene.name, gene.reactions)


    

    




ldhA frozenset({<Reaction LDH_D at 0x7f8f21a26208>})
dld frozenset({<Reaction LDH_D at 0x7f8f21a26208>})

In [65]:

    

mutant4 = model.copy()
mutant4.reactions.ACALD.knock_out()
mutant4.reactions.LDH_D.knock_out()
mutant4.reactions.ALCD2x.knock_out()


    

In [66]:

    

ppp = phenotypic_phase_plane(mutant4,
                             variables=[mutant4.reactions.BIOMASS_Ecoli_core_w_GAM],
                             objective=mutant4.reactions.EX_succ_e)

ppp.plot()


    

In [ ]: