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BIOMD0000000206 - Wolf2000_Glycolytic_Oscillations

 

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Reference Publication
Publication ID: 10692304
Wolf J, Passarge J, Somsen OJ, Snoep JL, Heinrich R, Westerhoff HV.
Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.
Biophys. J. 2000 Mar; 78(3): 1145-1153
Humboldt University, Institute of Biology, Theoretical Biophysics, Invalidenstrasse 42, D-10115 Berlin, Germany.  [more]
Model
Original Model: JWS logo
Submitter: Harish Dharuri
Submission ID: MODEL3352181362
Submission Date: 27 Nov 2008 17:53:21 UTC
Last Modification Date: 05 Jul 2012 14:48:43 UTC
Creation Date: 06 Oct 2008 20:39:38 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:is KEGG Pathway Glycolysis / Gluconeogenesis - Saccharomyces cerevisiae (budding yeast)
bqbiol:isVersionOf Gene Ontology glycolytic process
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

Model reproduces the dynamics of ATP and NADH as depicted in Fig 4 of the paper. Model successfully tested on Jarnac and MathSBML.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 10692304 Submission Date: 27 Nov 2008 17:53:21 UTC Last Modification Date: 05 Jul 2012 14:48:43 UTC Creation Date: 06 Oct 2008 20:39:38 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
v5 v7 v8 v9
v10 v6 v0  
Physical entities
Compartments Species
compartment Glucose ATP F16P
Triose_Gly3Phos_DHAP NAD 3PG
Pyruvate Acetaldehyde extracellular acetaldehyde
Global parameters
k0 k1 k2 k31
k33 k32 k34 k4
k5 k6 k7 k8
k9 k10 atot ntot
n ki    
Reactions (11)
 
 v1 [Glucose] + 2.0 × [ATP] ↔ [F16P];  
 
 v2 [F16P] ↔ 2.0 × [Triose_Gly3Phos_DHAP];  
 
 v3 [Triose_Gly3Phos_DHAP] + [NAD] ↔ [3PG] + [ATP];  
 
 v4 [3PG] ↔ [Pyruvate] + [ATP];  
 
 v5 [Pyruvate] ↔ [Acetaldehyde];  
 
 v7 [ATP] ↔ ;  
 
 v8 [Triose_Gly3Phos_DHAP] ↔ [NAD];  
 
 v9 [extracellular acetaldehyde] ↔ ;  
 
 v10 [Acetaldehyde] ↔ 0.1 × [extracellular acetaldehyde];  
 
 v6 [Acetaldehyde] ↔ [NAD];  
 
 v0  ↔ [Glucose];  
 
   compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose
Compartment: compartment
Initial concentration: 1.0
 
 ATP
Compartment: compartment
Initial concentration: 2.0
 
 F16P
Compartment: compartment
Initial concentration: 5.0
 
 Triose_Gly3Phos_DHAP
Compartment: compartment
Initial concentration: 0.6
 
 NAD
Compartment: compartment
Initial concentration: 0.6
 
 3PG
Compartment: compartment
Initial concentration: 0.7
 
 Pyruvate
Compartment: compartment
Initial concentration: 8.0
 
 Acetaldehyde
Compartment: compartment
Initial concentration: 0.08
 
 extracellular acetaldehyde
Compartment: compartment
Initial concentration: 0.02
 
Global Parameters (18)
 
   k0
Value: 50.0   (Units: mM_min_1)
Constant
 
   k1
Value: 550.0   (Units: mM_1_min_1)
Constant
 
   k2
Value: 9.8   (Units: min_1)
Constant
 
   k31
Value: 323.8   (Units: mM_1_min_1)
Constant
 
   k33
Value: 57823.1   (Units: mM_1_min_1)
Constant
 
   k32
Value: 76411.1   (Units: mM_1_min_1)
Constant
 
   k34
Value: 23.7   (Units: mM_1_min_1)
Constant
 
   k4
Value: 80.0   (Units: mM_1_min_1)
Constant
 
   k5
Value: 9.7   (Units: min_1)
Constant
 
   k6
Value: 2000.0   (Units: mM_1_min_1)
Constant
 
   k7
Value: 28.0   (Units: min_1)
Constant
 
   k8
Value: 85.7   (Units: mM_1_min_1)
Constant
 
   k9
Value: 80.0   (Units: min_1)
Constant
 
   k10
Value: 375.0   (Units: min_1)
Constant
 
   atot
Value: 4.0   (Units: mM)
Constant
 
   ntot
Value: 1.0   (Units: mM)
Constant
 
   n
Value: 4.0   (Units: dimensionless)
Constant
 
   ki
Value: 1.0   (Units: mM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000206

Curator's comment: (updated: 27 Nov 2008 17:53:04 GMT)

Result shown correspond to ATP and NADH dynamics as depicted in Fig 4 of the paper. Simulation result obtained using Jarnac

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