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BIOMD0000000042 - Nielsen1998_Glycolysis

 

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Reference Publication
Publication ID: 17029704
Nielsen K, Sørensen PG, Hynne F, Busse HG.
Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations.
Biophys. Chem. 1998 May; 72(1-2): 49-62
Department of Chemistry and CATS, H.C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.  [more]
Model
Original Model: BIOMD0000000042.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6622455387
Submission Date: 13 Sep 2005 14:43:11 UTC
Last Modification Date: 06 Jun 2013 11:35:59 UTC
Creation Date: 30 Jun 2005 14:08:28 UTC
Encoders:  Nicolas Le Novère
   Christoph Flamm
   Lukas Endler
set #1
bqmodel:isDerivedFrom PubMed 8061224
PubMed 6454892
set #2
bqbiol:isVersionOf Gene Ontology glycolytic process
bqbiol:is KEGG Pathway sce00010
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
bqbiol:isHomologTo Reactome REACT_1383
Notes

This model was automatically converted from model BIOMD0000000042 by using libSBML .

According to the BioModels Database terms of use , this generated model is not related with model BIOMD0000000042 any more.

Model
Publication ID: 17029704 Submission Date: 13 Sep 2005 14:43:11 UTC Last Modification Date: 06 Jun 2013 11:35:59 UTC Creation Date: 30 Jun 2005 14:08:28 UTC
Mathematical expressions
Reactions
ATPflow ADPflow NADHflow NADflow
GLCflow F6Pflow FBPflow GAPflow
DPGflow PEPflow PYRflow ACAflow
EtOHflow AMPflow Pflow reaction_1
reaction_2 reaction_3 reaction_4 reaction_5
reaction_6 reaction_7 reaction_8 reaction_9
reaction_10      
Physical entities
Compartments Species
compartment ATP ADP AMP
GLC F6P FBP
GAP NAD NADH
DPG PEP PYR
ACA EtOH P
Global parameters
V1 K1GLC K1ATP V2
K2 k2 K2ATP k3f
k3b V4 K4GAP K4NAD
k5f k5b V6 K6PEP
K6ADP V7 K7PYR k8f
k8b k9f k9b k10
flow      
Reactions (25)
 
 ATPflow  ↔ [ATP];  
 
 ADPflow  ↔ [ADP];  
 
 NADHflow  ↔ [NADH];  
 
 NADflow  ↔ [NAD];  
 
 GLCflow  ↔ [GLC];  
 
 F6Pflow [F6P] → ;  
 
 FBPflow [FBP] → ;  
 
 GAPflow [GAP] → ;  
 
 DPGflow [DPG] → ;  
 
 PEPflow [PEP] → ;  
 
 PYRflow [PYR] → ;  
 
 ACAflow [ACA] → ;  
 
 EtOHflow [EtOH] → ;  
 
 AMPflow [AMP] → ;  
 
 Pflow [P] → ;  
 
 reaction_1 [GLC] + [ATP] → [F6P] + [ADP];  
 
 reaction_2 [F6P] + [ATP] → [FBP] + [ADP];   {AMP}
 
 reaction_3 [FBP] ↔ 2.0 × [GAP];  
 
 reaction_4 [GAP] + [NAD] → [DPG] + [NADH];  
 
 reaction_5 [DPG] + [ADP] ↔ [PEP] + [ATP];  
 
 reaction_6 [PEP] + [ADP] → [PYR] + [ATP];  
 
 reaction_7 [PYR] → [ACA];  
 
 reaction_8 [ACA] + [NADH] ↔ [EtOH] + [NAD];  
 
 reaction_9 [AMP] + [ATP] ↔ 2.0 × [ADP];  
 
 reaction_10 [F6P] → [P];  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 ATP
Compartment: compartment
Initial amount: 4.49064
 
 ADP
Compartment: compartment
Initial amount: 0.108367
 
 AMP
Compartment: compartment
Initial amount: 0.00261149
 
 GLC
Compartment: compartment
Initial amount: 0.0112817
 
 F6P
Compartment: compartment
Initial amount: 0.65939
 
 FBP
Compartment: compartment
Initial amount: 0.00770135
 
 GAP
Compartment: compartment
Initial amount: 0.00190919
 
 NAD
Compartment: compartment
Initial amount: 3.62057
 
 NADH
Compartment: compartment
Initial amount: 0.616118
 
 DPG
Compartment: compartment
Initial amount: 0.299109
 
 PEP
Compartment: compartment
Initial amount: 0.0021125
 
 PYR
Compartment: compartment
Initial amount: 0.00422702
 
 ACA
Compartment: compartment
Initial amount: 0.0738334
 
 EtOH
Compartment: compartment
Initial amount: 0.33981
 
   P
Compartment: compartment
Initial amount: 0.0
 
Global Parameters (25)
 
   V1
Value: 0.5
Constant
 
   K1GLC
Value: 0.1
Constant
 
   K1ATP
Value: 0.063
Constant
 
   V2
Value: 1.5
Constant
 
   K2
Value: 0.0016
Constant
 
   k2
Value: 0.017
Constant
 
   K2ATP
Value: 0.01
Constant
 
   k3f
Value: 1.0
Constant
 
   k3b
Value: 50.0
Constant
 
   V4
Value: 10.0
Constant
 
   K4GAP
Value: 1.0
Constant
 
   K4NAD
Value: 1.0
Constant
 
   k5f
Value: 1.0
Constant
 
   k5b
Value: 0.5
Constant
 
   V6
Value: 10.0
Constant
 
   K6PEP
Value: 0.2
Constant
 
   K6ADP
Value: 0.3
Constant
 
   V7
Value: 2.0
Constant
 
   K7PYR
Value: 0.3
Constant
 
   k8f
Value: 1.0
Constant
 
   k8b
Value: 1.43E-4
Constant
 
   k9f
Value: 10.0
Constant
 
   k9b
Value: 10.0
Constant
 
   k10
Value: 0.05
Constant
 
   flow
Value: 0.011
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000042

Curator's comment: (updated: 30 Nov 2012 14:49:16 GMT)

Figure 9d of the paper reproduced using COPASI 4.8 (build 35).

Additional file(s)
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