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SysBioChalmers / GECKO

Toolbox for including enzyme constraints on a genome-scale model.
http://sysbiochalmers.github.io/GECKO/
MIT License
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Using GECKO for HumanGEM #129

Closed ezgitas closed 3 years ago

ezgitas commented 3 years ago

I am using GECKO to obtain the enzyme constraint HumanGEM model but most of the files are written for the saccharomyces cerevisiae model. I am having problems with adapting the toolbox to HumanGEM.

BenjaSanchez commented 3 years ago

@ezgitas hi there, thank you for showing interest in GECKO. I would recommend taking a look at the ecModels repository, where an enzyme-constrained model of humanGEM has already been developed. You can also see in general how we adapt the file structure to suit other organisms:

https://github.com/SysBioChalmers/ecModels/tree/feat/add_ecHumanGEM/ecHumanGEM

@IVANDOMENZAIN is this the latest version of ecHumanGEM?

IVANDOMENZAIN commented 3 years ago

Hi @ezgitas! you can find the latest version of the enzyme-constrained humanGEM in this link.

If you would like to generate cell-line specific or tissue-specific models for simulation purposes, then we recommend you to obtain those subset models first, by using some kind of gene expression data, and the tINIT algorithm available in the RAVEN toolbox. The next step would be to map your context-specific human model to ecHumanGEM in order to get your specific model with enzyme constraints, for this step we have generated a GECKO utility that gets this done in a matter of seconds, you can find it here.