Determining the Stoichiometry Matrix for a Model

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What Is a Stoichiometry Matrix? Example — Retrieving a Stoichiometry Matrix for a Model

What Is a Stoichiometry Matrix?

A stoichiometry matrix lets you easily determine:

• The reactants and products in a specific reaction in a model, including the stoichiometric value of the reactants and products

• The reactions that a specific species is part of, and whether the species is a reactant or product in that reaction

A stoichiometry matrix is an M-by-N matrix, where M equals the total number of reactions in a model, and N equals the total number of species in a model. Each row corresponds to a species, and each column corresponds to a reaction.

The matrix indicates which species and reactions are involved as reactants and products:

• Reactants are represented in the matrix with their stoichiometric value at the appropriate location (row of species, column of reaction). Reactants appear as negative values.

• Products are represented in the matrix with their stoichiometric value at the appropriate location (row of species, column of reaction). Products appear as positive values.

• All other locations in the matrix contain a 0.

For example, consider a model object containing two reactions. One reaction (named R1) is equal to 2 A + B -> 3 C, and the other reaction (named R2) is equal to B + 3 D -> 4 A. The stoichiometry matrix is:

      R1   R2
A     -2    4
B     -1   -1
C      3    0
D      0   -3

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Example — Retrieving a Stoichiometry Matrix for a Model

Retrieve a stoichiometry matrix for a model by passing the model object as an input argument to the getstoichmatrix method.

1. Read in m1, a model object, using sbmlimport:

   m1 = sbmlimport('lotka.xml');

2. Get the stoichiometry matrix for m1:

   [M,objSpecies,objReactions] = getstoichmatrix(m1)
   
   M =
   
      (2,1)        1
      (2,2)       -1
      (3,2)        1
      (3,3)       -1
      (4,3)        1
   
   
   objSpecies = 
   
       'x'
       'y1'
       'y2'
       'z'
   
   
   objReactions = 
   
       'Reaction1'
       'Reaction2'
       'Reaction3'

3. Convert the stoichiometry matrix from a sparse matrix to a full matrix to more easily see the relationships between species and reactions:

   M_full = full(M)

   M_full =
   
        0     0     0
        1    -1     0
        0     1    -1
        0     0     1

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Determining the Adjacency Matrix for a Model

Simulation and Analysis

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