calculating EFMs or basis vectors of null space

[Ehsan Zangeneh]

Hi

Recently I get familiar with CNA and don't know how to use it (I have its manual), so I have so much confusion, sorry for silly questions.

1- Does CNA use cobra based model like Recon 3D as input model ?

2- If yes, is it possible to use CNA to calculate EFMs or basis vectors of null space of Recon 3D model (with almost 10000 rxns on a regular laptop with 8 thread 3 GHz and 32 gig ram in a normal computation cost) in different conditions to compare those conditions in an unbiased manner or you suggest a better method ?

BR

Ehsan

[Steffen]

Dear Ehsan,

1) We have not used Recon3D in CellNetAnalyzer so far but, in principle, you could
 create a project by importing the SBML file of Recon3D.

2) Basis vectors of the nullspace of Recon3D will be computable (at least at a PC
with sufficient memory) while computation of EFMs will certainly not be feasible
due to combinatorial explosion.

Hope this helps.

[Ehsan Zangeneh]

Dear Steffen

Thank you for you clear answers, for sure it helps me.

BTW let me ask another question:

So as you mentioned because of combinatorial explosion calculation of all EFMs (EFVs) of big model with 10600 rxn is not possible, but in CNA is there any way to convert a big model into a smaller size through splitting it ?

I know I have to be careful of mass balance and some other steady state constraints in new model, so is there any built in function or protocol to do it in an automatic manner or any tutorial which explained how to do it as fast as possible ?

It would be great if there is a biological philosophy behind it, like splitting model into its cellular compartment, then I want its ribosomal and mitochondrial rxns in new reduced model.

BR

Ehsan

[Steffen]

Hi Ehsan,

you may use the NetworkReducer functionality of CNA. A paper on this method
can be found here:

https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-015-0191-x

Best regards,
Steffen.