support for the latest yeast model?

[jlerman44]

I'm trying to get set up with the Yeast model, but it seems the yeast models do not produce biomass when simulating using cobrapy. Its probably something stupid.

I got the latest yeast model from http://sourceforge.net/projects/yeast/files/yeast_7.1.zip/download

(I tried others as well)

then I ran:
from cobra.io.sbml import create_cobra_model_from_sbml_file

yeast_model = 'yeast_7.1_cobra.xml'
cobra_model = create_cobra_model_from_sbml_file(yeast_model, print_time=True)
cobra_model.optimize(solver='glpk')
print '\nSimulated growth rate is %1.3f' % cobra_model.solution.f

and got the output:
"Simulated growth rate is nan"

Their readme states that the answer should have been:
maximal growth rate: 0.13975 flux units

Any ideas? If not, I'll dig into it in a bit. Don't have a MATLAB license to check the answer using the original cobra toolbox.

Josh

[danielhyduke]

I think that the problem arises from using 'INF' and '-INF' as upper and lower bounds in the SBML file. I believe that Ali and I discussed using the default infinite upper and lower bounds from the COBRA Toolbox (1000, -1000) as the preliminary fix. Haven't had a chance to add a pull request with the fix.

[jlerman44]

Thanks. That worked. I can get back to baking bread now. I can look into fixing it if you'd like.

[PiotrZakrzewski]

Hi Josh,

The thing with yeast7 model is that constrainsts are defined there using
FBC which is not yet supported by cobra pie. If read and set them manualy
it will work - then you can save this model for later use.
I am also working with yeast7 and cobra pie so if you have any questions go
ahead.

Grtz
Piotrek
On Jan 8, 2014 9:31 PM, "Joshua Lerman" notifications@github.com wrote:

I'm trying to get set up with the Yeast model, but it seems the yeast
models do not produce biomass when simulating using cobrapy. Its probably
something stupid.

I got the latest yeast model from
http://sourceforge.net/projects/yeast/files/yeast_7.1.zip/download

(I tried others as well)

then I ran:
from cobra.io.sbml import create_cobra_model_from_sbml_file

yeast_model = 'yeast_7.1_cobra.xml'
cobra_model = create_cobra_model_from_sbml_file(yeast_model,
print_time=True)
cobra_model.optimize(solver='glpk')
print '\nSimulated growth rate is %1.3f' % cobra_model.solution.f

and got the output:
"Simulated growth rate is nan"

Their readme states that the answer should have been:
maximal growth rate: 0.13975 flux units

Any ideas? If not, I'll dig into it in a bit. Don't have a MATLAB license
to check the answer using the original cobra toolbox.

Josh

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Reply to this email directly or view it on GitHubhttps://github.com//issues/54
.

[aebrahim]

Fixed in 8a5b427