how to use stoichiometry matrix in matlab simbiology to construct model?

Hi, I got a stoichiometry matrix and other specification for a biological model. I wonder how to re-generate the model using this stoichiometry matrix?

link for the paper is http://www.ncbi.nlm.nih.gov/pubmed/?term=the+development+of+a+fully-integrated+immune+response+model(FIRM)+simulator+of+the+immune+response+through+integration+of+multiple+subset+models

link for the matrix is in its supplementary data

Thanks!

Answer 1

[Arthur Goldsipe]

SimBiology allows you to view the stoichiometric matrix for a model using getstoichmatrix. Unfortunately, SimBiology does not currently allow you to construct a model directly from the stoichiometric matrix. You can set/change the stoichiometry for individual reactions. However, that requires you to first define the reactants and products for a reaction, so I don't think this would be particularly helpful for you.

I also noticed a few problems with the stoichiometry matrix in the supplemental information. First, the file only includes an image of the matrix, not the numbers themselves. Second, the matrix appears to include several variables that I could not find values for (for example, numbac).

Personally, I recommend contacting the authors to request sufficient information to implement the model. Perhaps they can provide you with actual numeric values for the stoichiometry matrix or even a reference implementation of the model.

-Arthur