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The BiGG Models website server
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pH #285

Closed silviamorins closed 6 years ago

silviamorins commented 6 years ago

Hi, I would like to have a general information I was't able to find around: according to which pH value have the charges been assigned to the molecules in BiGG models?

jlerman44 commented 6 years ago

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261703/

For iJO1366 we used ph 7.2

Josh

On Mon, Feb 19, 2018 at 3:33 AM silviamorins notifications@github.com wrote:

Hi, I would like to have a general information I was't able to find around: according to which pH value have the charges been assigned to the molecules in BiGG models?

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zakandrewking commented 6 years ago

Yes, each model has its own set of charges, so you'll have to look in the source publications to find out.

(Thanks @jlerman44 for checking on iJO1366)

silviamorins commented 6 years ago

Thank you for your answer; however, I did probably not explain myself to a full extent: when I look up a Universal metabolite, I only find one charge value appointed to it, even if he is present in different models. I am wondering how this one particular value is assigned.

zakandrewking commented 6 years ago

There are a couple hundred with different charges in the models, in which case we list both on the universal page:

http://bigg.ucsd.edu/universal/metabolites/4hphac