2. Building a Model

This simple example demonstrates how to create a model, create a reaction, and then add the reaction to the model.

We’ll use the ‘3OAS140’ reaction from the STM_1.0 model:

1.0 malACP[c] + 1.0 h[c] + 1.0 ddcaACP[c] \(\rightarrow\) 1.0 co2[c] + 1.0 ACP[c] + 1.0 3omrsACP[c]

First, create the model and reaction.

In [1]:

from cobra import Model, Reaction, Metabolite
# Best practise: SBML compliant IDs
cobra_model = Model('example_cobra_model')

reaction = Reaction('3OAS140')
reaction.name = '3 oxoacyl acyl carrier protein synthase n C140 '
reaction.subsystem = 'Cell Envelope Biosynthesis'
reaction.lower_bound = 0.  # This is the default
reaction.upper_bound = 1000.  # This is the default
reaction.objective_coefficient = 0. # this is the default

We need to create metabolites as well. If we were using an existing model, we could use get_by_id to get the apporpriate Metabolite objects instead.

In [2]:

ACP_c = Metabolite(
    'ACP_c',
    formula='C11H21N2O7PRS',
    name='acyl-carrier-protein',
    compartment='c')
omrsACP_c = Metabolite(
    '3omrsACP_c',
    formula='C25H45N2O9PRS',
    name='3-Oxotetradecanoyl-acyl-carrier-protein',
    compartment='c')
co2_c = Metabolite(
    'co2_c',
    formula='CO2',
    name='CO2',
    compartment='c')
malACP_c = Metabolite(
    'malACP_c',
    formula='C14H22N2O10PRS',
    name='Malonyl-acyl-carrier-protein',
    compartment='c')
h_c = Metabolite(
    'h_c',
    formula='H',
    name='H',
    compartment='c')
ddcaACP_c = Metabolite(
    'ddcaACP_c',
    formula='C23H43N2O8PRS',
    name='Dodecanoyl-ACP-n-C120ACP',
    compartment='c')

Adding metabolites to a reaction requires using a dictionary of the metabolites and their stoichiometric coefficients. A group of metabolites can be added all at once, or they can be added one at a time.

In [3]:

reaction.add_metabolites({malACP_c: -1.0,
                          h_c: -1.0,
                          ddcaACP_c: -1.0,
                          co2_c: 1.0,
                          ACP_c: 1.0,
                          omrsACP_c: 1.0})


reaction.reaction  # This gives a string representation of the reaction

Out[3]:

'ddcaACP_c + h_c + malACP_c --> 3omrsACP_c + ACP_c + co2_c'

The gene_reaction_rule is a boolean representation of the gene requirements for this reaction to be active as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307. We will assign the gene reaction rule string, which will automatically create the corresponding gene objects.

In [4]:

reaction.gene_reaction_rule = '( STM2378 or STM1197 )'
reaction.genes

Out[4]:

frozenset({<Gene STM2378 at 0x7fada4592908>, <Gene STM1197 at 0x7fada45927f0>})

At this point in time, the model is still empty

In [5]:

print('%i reactions initially' % len(cobra_model.reactions))
print('%i metabolites initially' % len(cobra_model.metabolites))
print('%i genes initially' % len(cobra_model.genes))

0 reactions initially
0 metabolites initially
0 genes initially

We will add the reaction to the model, which will also add all associated metabolites and genes

In [6]:

cobra_model.add_reaction(reaction)

# Now there are things in the model
print('%i reaction' % len(cobra_model.reactions))
print('%i metabolites' % len(cobra_model.metabolites))
print('%i genes' % len(cobra_model.genes))

1 reaction
6 metabolites
2 genes

We can iterate through the model objects to observe the contents

In [7]:

# Iterate through the the objects in the model
print("Reactions")
print("---------")
for x in cobra_model.reactions:
    print("%s : %s" % (x.id, x.reaction))

print("")
print("Metabolites")
print("-----------")
for x in cobra_model.metabolites:
    print('%9s : %s' % (x.id, x.formula))

print("")
print("Genes")
print("-----")
for x in cobra_model.genes:
    associated_ids = (i.id for i in x.reactions)
    print("%s is associated with reactions: %s" %
          (x.id, "{" + ", ".join(associated_ids) + "}"))

Reactions
---------
3OAS140 : ddcaACP_c + h_c + malACP_c --> 3omrsACP_c + ACP_c + co2_c

Metabolites
-----------
3omrsACP_c : C25H45N2O9PRS
ddcaACP_c : C23H43N2O8PRS
    ACP_c : C11H21N2O7PRS
    co2_c : CO2
 malACP_c : C14H22N2O10PRS
      h_c : H

Genes
-----
STM2378 is associated with reactions: {3OAS140}
STM1197 is associated with reactions: {3OAS140}