Database for bioinformatical applications

Question

[kovszasz]

Does anyone know a database or a website, where I can find growth mediums, that can be used for bioinformatical simulations? I've joined a research group where we use cobrapy python package and I have to simulate in silico such experiments, which were done in vitro. I can create my own database of growth mediums, but it would help me a lot and save time. Any help here would be appreciated! :)

[GenoMax]

Just so we are clear .. you are asking for a database of growth media chemical compositions so that you can do flux balance analysis and such? If yes, then change the title to reflect that need.

[natasha.sernova]

As far as I have understood, you are looking for something like that.

See one Biostars post and one article:

FBA to simulate bacteria growth on different growth medium

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123892/

And even this additional article:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171303/

Answer 1

[Moritz E. Beber]

If you are working with E. coli http://prokaryomics.com/ contains quite a wealth of data. In our work for the DD-DeCaF project, we have integrated the prokaryomics data sets in our platform app.dd-decaf.eu where you can apply them to basic simulations of E. coli models.