def room_model():
"""
Generate ROOM model as described in [1]_
References
----------
.. [1] Tomer Shlomi, Omer Berkman and Eytan Ruppin, "Regulatory on/off
minimization of metabolic flux changes after genetic perturbations",
PNAS 2005 102 (21) 7695-7700; doi:10.1073/pnas.0406346102
"""
test_model = Model("papin_2003")
v_1 = Reaction("v1")
v_2 = Reaction("v2")
v_3 = Reaction("v3")
v_4 = Reaction("v4")
v_5 = Reaction("v5")
v_6 = Reaction("v6", upper_bound=0.0)
b_1 = Reaction("b1", upper_bound=10.0, lower_bound=0.0)
b_2 = Reaction("b2")
b_3 = Reaction("b3")
test_model.add_reactions([v_1, v_2, v_3, v_4, v_5, v_6, b_1, b_2, b_3])
v_1.reaction = "A -> B"
v_2.reaction = "2 B -> C + byp"
v_3.reaction = "2 B + cof -> D"
v_4.reaction = "D -> E + cof"
v_5.reaction = "C + cof -> D"
v_6.reaction = "C -> E"
b_1.reaction = "-> A"
b_2.reaction = "E ->"
b_3.reaction = "byp ->"
test_model.objective = 'b2'
return test_model
def room_model():
"""
Generate ROOM model as described in [1]_
References
----------
.. [1] Tomer Shlomi, Omer Berkman and Eytan Ruppin, "Regulatory on/off
minimization of metabolic flux changes after genetic perturbations",
PNAS 2005 102 (21) 7695-7700; doi:10.1073/pnas.0406346102
"""
test_model = Model("papin_2003")
v_1 = Reaction("v1")
v_2 = Reaction("v2")
v_3 = Reaction("v3")
v_4 = Reaction("v4")
v_5 = Reaction("v5")
v_6 = Reaction("v6", upper_bound=0.0)
b_1 = Reaction("b1", upper_bound=10.0, lower_bound=0.0)
b_2 = Reaction("b2")
b_3 = Reaction("b3")
test_model.add_reactions([v_1, v_2, v_3, v_4, v_5, v_6, b_1, b_2, b_3])
v_1.reaction = "A -> B"
v_2.reaction = "2 B -> C + byp"
v_3.reaction = "2 B + cof -> D"
v_4.reaction = "D -> E + cof"
v_5.reaction = "C + cof -> D"
v_6.reaction = "C -> E"
b_1.reaction = "-> A"
b_2.reaction = "E ->"
b_3.reaction = "byp ->"
test_model.objective = 'b2'
return test_model
def construct_papin_2003_model():
test_model = Model("papin_2003")
v1 = Reaction("v1")
v2 = Reaction("v2")
v3 = Reaction("v3")
v4 = Reaction("v4")
v5 = Reaction("v5")
v6 = Reaction("v6", upper_bound=0.0)
b1 = Reaction("b1", upper_bound=10.0, lower_bound=0.0)
b2 = Reaction("b2")
b3 = Reaction("b3")
test_model.add_reactions([v1, v2, v3, v4, v5, v6, b1, b2, b3])
v1.reaction = "A -> B"
v2.reaction = "2 B -> C + byp"
v3.reaction = "2 B + cof -> D"
v4.reaction = "D -> E + cof"
v5.reaction = "C + cof -> D"
v6.reaction = "C -> E"
b1.reaction = "-> A"
b2.reaction = "E ->"
b3.reaction = "byp ->"
test_model.objective = 'b2'
return test_model
def construct_papin_2003_model():
test_model = Model("papin_2003")
v1 = Reaction("v1")
v2 = Reaction("v2")
v3 = Reaction("v3")
v4 = Reaction("v4")
v5 = Reaction("v5")
v6 = Reaction("v6", upper_bound=0.0)
b1 = Reaction("b1", upper_bound=10.0, lower_bound=0.0)
b2 = Reaction("b2")
b3 = Reaction("b3")
test_model.add_reactions([v1, v2, v3, v4, v5, v6, b1, b2, b3])
v1.reaction = "A -> B"
v2.reaction = "2 B -> C + byp"
v3.reaction = "2 B + cof -> D"
v4.reaction = "D -> E + cof"
v5.reaction = "C + cof -> D"
v6.reaction = "C -> E"
b1.reaction = "-> A"
b2.reaction = "E ->"
b3.reaction = "byp ->"
test_model.objective = 'b2'
return test_model
