def build_model():
m = SolverBasedModel("Blazier et al 2012")
m1_e = Metabolite("M1_e")
m1 = Metabolite("M1")
m2 = Metabolite("M2")
m3 = Metabolite("M3")
m4_e = Metabolite("M4_e")
m4 = Metabolite("M4")
m5 = Metabolite("M5")
r1 = Reaction("R1")
r1.add_metabolites({m1_e: -1, m1: 1})
r2 = Reaction("R2")
r2.add_metabolites({m1: -1, m2: 1})
r2.gene_reaction_rule = "Gene2"
r3 = Reaction("R3")
r3.add_metabolites({m2: -1, m3: 1})
r3.gene_reaction_rule = "Gene3"
r4 = Reaction("R4")
r4.add_metabolites({m3: -1})
r5 = Reaction("R5")
r5.add_metabolites({m4_e: -1, m4: 1})
r6 = Reaction("R6")
r6.add_metabolites({m4: -1, m5: 1})
r6.gene_reaction_rule = "Gene6"
r7 = Reaction("R7")
r7.add_metabolites({m5: -1, m2: 1})
r7.lower_bound = -r7.upper_bound
r7.gene_reaction_rule = "Gene7"
r8 = Reaction("R8")
r8.add_metabolites({m5: -1})
m.add_reactions([r1, r2, r3, r4, r5, r6, r7, r8])
EX_M1_e = m.add_demand(m1_e, "EX_")
EX_M1_e.lower_bound = -10
EX_M4_e = m.add_demand(m4_e, "EX_")
EX_M4_e.lower_bound = -10
m.objective = r4
return m
def build_model():
m = SolverBasedModel("Blazier et al 2012")
m1_e = Metabolite("M1_e")
m1 = Metabolite("M1")
m2 = Metabolite("M2")
m3 = Metabolite("M3")
m4_e = Metabolite("M4_e")
m4 = Metabolite("M4")
m5 = Metabolite("M5")
r1 = Reaction("R1")
r1.add_metabolites({m1_e: -1, m1: 1})
r2 = Reaction("R2")
r2.add_metabolites({m1: -1, m2: 1})
r2.gene_reaction_rule = "Gene2"
r3 = Reaction("R3")
r3.add_metabolites({m2: -1, m3: 1})
r3.gene_reaction_rule = "Gene3"
r4 = Reaction("R4")
r4.add_metabolites({m3: -1})
r5 = Reaction("R5")
r5.add_metabolites({m4_e: -1, m4: 1})
r6 = Reaction("R6")
r6.add_metabolites({m4: -1, m5: 1})
r6.gene_reaction_rule = "Gene6"
r7 = Reaction("R7")
r7.add_metabolites({m5: -1, m2: 1})
r7.lower_bound = -r7.upper_bound
r7.gene_reaction_rule = "Gene7"
r8 = Reaction("R8")
r8.add_metabolites({m5: -1})
m.add_reactions([r1, r2, r3, r4, r5, r6, r7, r8])
EX_M1_e = m.add_demand(m1_e, "EX_")
EX_M1_e.lower_bound = -10
EX_M4_e = m.add_demand(m4_e, "EX_")
EX_M4_e.lower_bound = -10
m.objective = r4
return m
def build_model():
m = SolverBasedModel("Zur et al 2012")
m1 = Metabolite("M1")
m2 = Metabolite("M2")
m3 = Metabolite("M3")
m4 = Metabolite("M4")
m5 = Metabolite("M5")
m6 = Metabolite("M6")
m7 = Metabolite("M7")
m8 = Metabolite("M8")
m9 = Metabolite("M9")
m10 = Metabolite("M10")
r1 = Reaction("R1")
r1.add_metabolites({m3: 1})
r2 = Reaction("R2")
r2.add_metabolites({m1: 1})
r2.gene_reaction_rule = "G1 or G2"
r3 = Reaction("R3")
r3.add_metabolites({m2: 1})
r3.gene_reaction_rule = "G5"
r4 = Reaction("R4")
r4.add_metabolites({m1: -1, m10: 1})
r4.lower_bound = -r4.upper_bound
r5 = Reaction("R5")
r5.add_metabolites({m10: -1, m4: 1})
r5.lower_bound = -r5.upper_bound
r6 = Reaction("R6")
r6.add_metabolites({m1: -1, m4: 1})
r7 = Reaction("R7")
r7.add_metabolites({m1: -1, m2: -1, m5: 1, m6: 1})
r7.gene_reaction_rule = "G6"
r8 = Reaction("R8")
r8.add_metabolites({m3: -1, m4: -1, m7: 1, m8: 1})
r8.gene_reaction_rule = "G3"
r9 = Reaction("R9")
r9.add_metabolites({m5: -1})
r10 = Reaction("R10")
r10.add_metabolites({m6: -1, m9: 1})
r10.gene_reaction_rule = "G7"
r11 = Reaction("R11")
r11.add_metabolites({m7: -1})
r12 = Reaction("R12")
r12.add_metabolites({m8: -1})
r12.gene_reaction_rule = "G4"
r13 = Reaction("R13")
r13.add_metabolites({m9: -1})
m.add_reactions([r1, r2, r3, r4, r5, r6, r7, r8])
m.objective = r4
return m
def build_model():
m = SolverBasedModel("Zur et al 2012")
m1 = Metabolite("M1")
m2 = Metabolite("M2")
m3 = Metabolite("M3")
m4 = Metabolite("M4")
m5 = Metabolite("M5")
m6 = Metabolite("M6")
m7 = Metabolite("M7")
m8 = Metabolite("M8")
m9 = Metabolite("M9")
m10 = Metabolite("M10")
r1 = Reaction("R1")
r1.add_metabolites({m3: 1})
r2 = Reaction("R2")
r2.add_metabolites({m1: 1})
r2.gene_reaction_rule = "G1 or G2"
r3 = Reaction("R3")
r3.add_metabolites({m2: 1})
r3.gene_reaction_rule = "G5"
r4 = Reaction("R4")
r4.add_metabolites({m1: -1, m10: 1})
r4.lower_bound = -r4.upper_bound
r5 = Reaction("R5")
r5.add_metabolites({m10: -1, m4: 1})
r5.lower_bound = -r5.upper_bound
r6 = Reaction("R6")
r6.add_metabolites({m1: -1, m4: 1})
r7 = Reaction("R7")
r7.add_metabolites({m1: -1, m2: -1, m5: 1, m6: 1})
r7.gene_reaction_rule = "G6"
r8 = Reaction("R8")
r8.add_metabolites({m3: -1, m4: -1, m7: 1, m8: 1})
r8.gene_reaction_rule = "G3"
r9 = Reaction("R9")
r9.add_metabolites({m5: -1})
r10 = Reaction("R10")
r10.add_metabolites({m6: -1, m9: 1})
r10.gene_reaction_rule = "G7"
r11 = Reaction("R11")
r11.add_metabolites({m7: -1})
r12 = Reaction("R12")
r12.add_metabolites({m8: -1})
r12.gene_reaction_rule = "G4"
r13 = Reaction("R13")
r13.add_metabolites({m9: -1})
m.add_reactions([r1, r2, r3, r4, r5, r6, r7, r8])
m.objective = r4
return m