Comments (4)
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.
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Thanks. That worked. I can get back to baking bread now. I can look into fixing it if you'd like.
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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" [email protected] 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_fileyeast_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.fand got the output:
"Simulated growth rate is nan"Their readme states that the answer should have been:
maximal growth rate: 0.13975 flux unitsAny 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
—
Reply to this email directly or view it on GitHubhttps://github.com//issues/54
.
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Fixed in 8a5b427
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Related Issues (20)
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