How do I create the seeds file for meneco?

[Yuanmaosen]

Hello!
I'm trying to reproduce a metabolic model from a published paper using Meneco, and I want to generate my own seed file to better understand the reconstruction workflow.

The authors wrote:

"In Meneco, target compounds correspond to metabolites present in the biomass function, while seed compounds are composed of metabolites present in the growth medium, plus some cofactors and metabolites required for FBA growth."

I have a draft model generated with RAVEN, and I’d like to know how to figure out what should be included in the seed file.

Is there a way to extract this directly from the draft model? Or should I define it manually based on the growth medium?

Any advice or example would be super helpful. Thanks a lot!

[cfrioux]

Hi, sorry for the delay before answering.

The draft model should not have any indication of a medium (would be modeled as export reactions).
So the best way to proceed would be to create the file based on the growth medium as you suggested.

If you struggle to create it manually, you can take a look at this command from another tool: https://metage2metabo.readthedocs.io/en/latest/tutorial.html#optional-create-the-seeds-sbml-file

You might also want to consider testing menace with or without adding a few cofactors / currency metabolites to the seeds (NAD, ADP, NADP...). Sometimes the de-novo producibility of such molecules blocks reachability of target metabolites.

Hope this helps a bit

[Yuanmaosen]

Thank you for the detailed explanation! This is very helpful.