Creating Biomodels-Compliant Sbml Model

Question

[robjohn7000]

Hi,

I have a file of metabolic network of reactions that I will like to turn into an SBML format (Level2: version 1/2/3/4). Does anyone know of the easiest way to get this done?

Thanks

[B. Arman Aksoy]

Can you give us a little bit more details on the type of information that you currently have? Do you have the metabolic reactions in a different format, e.g. BioPAX? Or do you just have a list of identification for some interactions of interest to you?

Do you know about the SBML toolbox documentation? Or about the RECON 2 model?

[robjohn7000]

I just have a list of chemical reactions. e.g A + B -> C + D. Yes, I'm aware of SBML toolbox

Answer 1

[B. Arman Aksoy]

I think you have two options here:

1) If the reactions that you have are not novel, in the sense that they have already been curated, then I suggest you extract subgraphs of the Recon 2 model and put them in a single model. On their website there is a place where you can search for known metabolites and/or reactions, e.g.: http://humanmetabolism.org/?page_id=5

2) If these reactions are special, in the sense that you cannot find them on the known curated models, then I suggest you use one of the modeling tools that support SBML exports. Your options include CellDesigner, PathVisio and VirtualCell (not sure whether the last one allows you curate models). Another possible approach is to do some coding with libSBML and create an application that parses your files and turns them into SBML model, but I guess it is relatively harder -- although much more scalable and preferable.

[robjohn7000]

Thanks a lot for your suggestions Arman.