Question: Database for bioinformatical applications
0
gravatar for kovszasz
19 months ago by
kovszasz0
kovszasz0 wrote:

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! :)

fba cobrapy • 666 views
ADD COMMENTlink modified 11 months ago by Moritz E. Beber0 • written 19 months ago by kovszasz0
1

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.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax67k
1

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/

ADD REPLYlink modified 17 months ago • written 17 months ago by natasha.sernova3.4k
0
gravatar for Moritz E. Beber
11 months ago by
DTU Biosustain, Copenhagen, Denmark
Moritz E. Beber0 wrote:

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.

ADD COMMENTlink written 11 months ago by Moritz E. Beber0
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