Getting started

Open BioOpt file

BioOpt library comes with a toy model (toy.bioopt) which will be used through the rest of this tutorial.

from bioopt.bioopt_parser import BiooptParser
from bioopt import toy_path

model = BiooptParser().parse_file(toy_path())
print(model)

Bioopt model contains a list of reactions reactions and a description of objective function (like biomass)

print("Total number of reactions: {0}".format(len(model.reactions)))
print("Objective: {0}".format(model.objective))

Total number of reactions: 11
Objective: R3 * 1.0 * 1.0

Retrieve reactions

Because reactions in BioOpt library are regular lists they can be accessed by index starting at 0. Additionally a a model can be searched for a specific reaction using reaction name or regular expression. Finally, there is a special function to search all export reactions

print(model.find_reaction("R1"))
print(model.find_reactions(["R1", "R2"]))
print(model.find_reactions(r".*xtI$", regex=True))
print("Model have {0} export/import reactions".format(len(model.find_boundary_reactions()))) # search for all export reactions

R1[-inf, inf]: 1 A <-> 2 B
[R1[-inf, inf]: 1 A <-> 2 B, R2[0, inf]: 1 A -> 1 C]
[A_xtI[0.0, 1.0]: 1 A_xtX* -> 1 A, B_xtI[0.0, 1.0]: 1 B_xtX* -> 1 B, C_xtI[0.0, 1.0]: 1 C_xtX* -> 1 C, D_xtI[0, inf]: 1 D_xtX* -> 1 D]
Model have 8 export/import reaction

Retrieve metabolites

Metabolites can not be accessed as a list but similar to reactions a model can be searched for specific metabolites using metabolite name or regular expression. And if you won’t provide any pattern for metabolite name all metabolites will be returned. Additionally, a model can be searched for a specific reaction using reaction name or regular expression. Finally, there is a special function to search all export reactions

print("Model contains {0} unique metabolites".format(len(model.find_metabolites())))
print(model.find_metabolite("A"))
print(model.find_metabolites(["B", "B_xtX"]))
print(model.find_metabolites(r"B.*", regex=True))

Model contains 8 unique metabolites
A
[B, B_xtX*]
[B, B_xtX*]

Access reaction information

Every reaction include flux constraints, directionality and list of reactants and products.

r = model.find_reaction("A_xtI")
print("Reaction '{react}' has direction {dir} and constraints from {lb} to {ub}".format(react=r.name, dir=r.direction, lb=r.bounds.lb, ub=r.bounds.ub))
print("Reactants: {0}".format(','.join(rs.metabolite.name for rs in r.reactants)))
print("Products: {0}".format(','.join(ps.metabolite.name for ps in r.products)))

Reaction 'A_xtI' has direction -> and constraints from 0.0 to 1.0
Reactants: A_xtX
Products: A

Access metabolite information

Every metabolite have information about its name and whether it is boundary (exported/imported) or balanced metabolite

m = model.find_metabolite("A_xtX")
print("Metabolite '{0}' is {1}boundary".format(m.name, "not " if not m.boundary else ""))

Metabolite 'A_xtX' is boundary

In context of reaction metabolites are wrapped inside ReactionMember class which allows access to a coefficient before metabolite in this reaction

r = model.find_reaction("A_xtI")
print("Metabolite {0} have coefficient {1:.0f}".format(r.reactants[0].metabolite, r.reactants[0].coefficient))

Metabolite A_xtX* have coefficient 1