The model reproduces Fig 6 of the paper. The stoichiometry and rate of reactions involving uptake of metabolites from extracellular medium have been changed corresponding to Yvol (ratio of extracellular volume to cytosolic volume) mentioned in the publication. The extracellular and cytosolic compartments have been set to 1. Concentration of extracellular glucose, GlcX, is set to 6.7 according to the equation for cellular glucose uptake rate in Table 7 of the paper. The model was successfully tested on MathSBML and Jarnac
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SBML
level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based
modelling using JWS Online
, Bioinformatics, 20:2143-2144
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This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use
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To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
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Full-scale model of glycolysis in Saccharomyces cerevisiae.
- F Hynne, S Danø, P G Sørensen
- Biophysical chemistry , 12/ 2001 , Volume 94 , Issue 1-2 , pages: 121-163 , PubMed ID: 11744196
- Department of Chemistry and CATS, H.C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark. fh@kiku.dk
- We present a powerful, general method of fitting a model of a biochemical pathway to experimental substrate concentrations and dynamical properties measured at a stationary state, when the mechanism is largely known but kinetic parameters are lacking. Rate constants and maximum velocities are calculated from the experimental data by simple algebra without integration of kinetic equations. Using this direct approach, we fit a comprehensive model of glycolysis and glycolytic oscillations in intact yeast cells to data measured on a suspension of living cells of Saccharomyces cerevisiae near a Hopf bifurcation, and to a large set of stationary concentrations and other data estimated from comparable batch experiments. The resulting model agrees with almost all experimentally known stationary concentrations and metabolic fluxes, with the frequency of oscillation and with the majority of other experimentally known kinetic and dynamical variables. The functional forms of the rate equations have not been optimized.
Submitter of this revision: Lucian Smith
Curator: Lucian Smith
Modeller: Nicolas Le Novère
Metadata information
BioModels Database MODEL6624167348
KEGG Pathway Glycolysis / Gluconeogenesis - Saccharomyces cerevisiae (budding yeast)
isDescribedBy (1 statement)
hasTaxon (1 statement)
isVersionOf (1 statement)
isHomologTo (1 statement)
hasProperty (1 statement)
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