예제 #1
0
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
예제 #2
0
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
예제 #3
0
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
예제 #4
0
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