Biomass Mantainance

[fgualdr]

Hi,

I am trying to use HumanGEM to perform cell type tailoring and FBA.
the cell type I am trying to model is a resting non-growing cell.
Could I ask if inbuilt in human there is a biomass mantainance that I can use?
Thanks in advance
Francesco

[JonathanRob]

Hi @fgualdr, yes, there are a few options one could use for maintenance:

• biomass_maintenance_Recon3D and biomass_maintenance_noTrTr_Recon3D originate from the Recon3D model, and could be used (the latter is without transcription or translation). Note that these reactions are currently inactivated in Human-GEM (ub = 0), so don't forget to open their bounds before using.
• HMR_3964 is just basic ATP hydrolysis, if you're interested in a more minimal maintenance cost.

[haowang-bioinfo]

@fgualdr Yes, Human-GEM includes several different biomass objective functions that were described in #63.

[JonathanRob]

I will convert this Issue to a "Discussion", since I think that is a better fit.