Looking for a commonly used fermentation pathway model

[Robert Ness]

Can anyone point me towards a canonical fermentation pathway (SBML file) that I can work with in Copasi?  I am trying to find a metabolic-engineering example, where one can evaluate the effects of interventions on enzymes has on downstream production of molecules in some microbial fermentation process.  I'm new to the space, and figured there must be some canonical example out there, so I figured I'd ask.  

[Pedro Mendes]

Robert,

A widely used model of yeast glycolysis (alcoholic fermentation) is the
Teusink et al. 2000 model which you can get the SBML file from the
BioModels database:

http://www.ebi.ac.uk/biomodels-main/BIOMD0000000064

if you prefer E.coli to yeast, then I would suggest the Millard et. al.
2017 model which we just recently published:

http://www.ebi.ac.uk/biomodels-main/MODEL1505110000

this one includes a larger portion of central metabolism, not just
glycolysis.

Pedro

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[Robert Ness]

Thank you Pedro!

On Wednesday, May 31, 2017 at 1:49:25 PM UTC-7, Pedro Mendes wrote:

Robert,

A widely used model of yeast glycolysis (alcoholic fermentation) is the
Teusink et al. 2000 model which you can get the SBML file from the
BioModels database:

http://www.ebi.ac.uk/biomodels-main/BIOMD0000000064

if you prefer E.coli to yeast, then I would suggest the Millard et. al.
2017 model which we just recently published:

http://www.ebi.ac.uk/biomodels-main/MODEL1505110000

this one includes a larger portion of central metabolism, not just
glycolysis.

Pedro


On 05/31/2017 03:08 PM, Robert Ness wrote:
> Can anyone point me towards a canonical fermentation pathway (SBML file)
> that I can work with in Copasi?  I am trying to find a
> metabolic-engineering example, where one can evaluate the effects of
> interventions on enzymes has on downstream production of molecules in
> some microbial fermentation process.  I'm new to the space, and figured
> there must be some canonical example out there, so I figured I'd ask.
>
> --
> You received this message because you are subscribed to the Google
> Groups "COPASI User Forum" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to copasi-user-fo...@googlegroups.com

> <mailto:copasi-user-forum+unsub...@googlegroups.com>.