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closeUnsufficient supplementary files
Posted by GKnittel on 24 May 2013 at 10:04 GMT
I am a little disappointed by the missing thoroughness of the supplied model files. The SBML file does not contain any information about kinetics. And the pdf that contains the rate equations is very unorganized and hard to read. Not even the orientation of the pages is right. Some equations I do not fully understand. For example, the description of Phosphofructo kinase 2: vpmax=vnmax. Now what is vnmax? And how is vdpmax defined? It is part of the equations, but does not get defined anywhere.
I was under the impression that if you publish a paper about a model in a computational biology journal, you should provide the model itself.
RE: Unsufficient supplementary files
mkoenig replied to GKnittel on 06 Apr 2014 at 13:46 GMT
I am aware, that the provided supplementary files were not sufficient to replicate the presented results.
Therefore, I provide additional supplementary files containing the SBML with kinetics (runnable in Copasi) as well as the matlab source code to generate the figure at
http://sourceforge.net/pr...
Clone the project via:
git clone git://git.code.sf.net/p/g... glucosemodel-code
SBML running in Copasi is available in the subfolder
/sbml/
The matlab model is in
/matlab/core_kinetic_model/
with
sim_single.m - running single simulation
dydt_model_glucose_sbml.m - ODEs for the model
RE: RE: Unsufficient supplementary files
mkoenig replied to mkoenig on 06 Jul 2017 at 10:10 GMT
Model supplementary information has been migrated to github
https://github.com/matthi...