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SysBioChalmers / yeast-GEM

The consensus GEM for Saccharomyces cerevisiae
http://sysbiochalmers.github.io/yeast-GEM/
Creative Commons Attribution 4.0 International
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What's the expected growth rate of yeast8? #275

Closed BeeAnka closed 2 years ago

BeeAnka commented 3 years ago

Hi, this is not an issue but a small question. I downloaded the yeast-GEM.xml model and would like to make sure that everything is fine before I start my analysis. Therefore I would like to confirm the "basic" features amount of reactions, metabolites, genes and growth rate. I found this information for the yeast 7.6 model but not for the yeast8. Here are my results: reactions: 4058, metabolites: 2742, genes: 1150 and growth rate from cobrapy standard FBA: 0.08374. It would be really helpful if you could confirm that these properties are correct or tell me if something went wrong during reading the model with cobrapy.

edkerk commented 3 years ago

Seems like you've successfully loaded yeast-GEM! I assume it's version 8.5.0?

BeeAnka commented 3 years ago

Yes, it's version 8.5.0 and I just wanted to make sure if the growth rate I get via cobrapy FBA is correct? Sorry, if these questions seems a bit stupid, but I'm quiet new to working with this kind of models.

edkerk commented 3 years ago

It's indeed the same growth rate as we get in MATLAB via RAVEN or COBRA.