#19 Regulatory FBA

[Ashish Sharma]

Hi,
Surely, It is a great tool. But I found that documentation for this tool is still very compact and thus for new beginners like me, it becomes difficult to understand the actual meaning of running the different kinds of simulations and understanding its results. I wish you will make even more detailed descriptions about each features in optflux.
Right now I am looking to run regulatory FBA model of E.coli model. As you suggested it supports SRFBA, which is really a good feature. But on the tutorial page only the toy model is given. I dont know from where to get the exact files of .fluxes, .matrix, .metlab, .gr, *.regnet for E.coli model.
Regards
Ashish

[Orlando Rocha]

Hello dear Ashish,

Thank you for exposing your comments and doubts, these will allow us to improve this tool. We know that the support documentation of the regulatory plugin is a little bit simplistic, however we will try to improve this documentation. Regarding to your main doubt, at the moment the regulatory plugin only supports the import of the metabolic models through a flat file format. Nevertheless, you can convert your metabolic model (SBML file), at the optflux, to a flat file format by doing the following steps:
In the OptFlux, create a "New Project" --> select "SBML" --> select your SBML file and click on the "next" button until the end of the loading process. After loading the model go to "File" (upper-left in the main menu), and click on "Export" and choose "Model to Flat Files". After this process, you have your model in a flat file format that can be used in the regulatory plugin. Concerning to the regulatory model, you have to build an extra text file containing the information of the genes, transcriptional factors and the boolean rules. This information must be described in the following manner: bnumber;genename;TFname;regulatory_rule
As an example, we want to describe 5 genes in the regulatory model, we write like this:

b4031;xylE;XylE;(XylR)
b2818;argA;ArgA;(NOT ArgR)
b2429;yfeV;YfeV;
b4024;lysC;LysC;(NOT lys-L(e)>0)
b3390;aroK;AroK;

We hope, that in the next release of the regulatory plugin, already can be possible to import the metabolic model directly from a SBML file, it is a priority in our improvement list.

I hope that I have helped you, and that you continue using successfully our tool in your work.

Best Regards
Orlando Rocha