292470
fast: false
reactant: 292494
reactant: 292482
type: Reaction
name: v9
product: 292518
reversible: true
product: 292506
is: SBO:0000176
kinetic law: 292530
notes: Krebs cycle

292299
stoichiometry: 1.0
species: meta s2 e1
type: SpeciesReference

293087
stoichiometry: 1.0
species: meta n2 e7
type: SpeciesReference

291932
units: dimensionless
value: 20.0
type: LocalParameter

291368
constant: true
units: dimensionless
value: 0.2
type: Parameter

291283
constant: true
size: 1.0
spatial dimensions: 3.0
type: Compartment

292976
stoichiometry: 3.0
species: meta a2
type: SpeciesReference

292287
kinetic law: 292348
reversible: true
reactant: 292299
fast: false
product: 292324
type: Reaction
is: SBO:0000176
product: 292336
notes: mitochondrial alpha-glycerophosphate reaction of H-transporter
name: v7
reactant: 292312

291883
stoichiometry: 1.0
species: meta r2
type: SpeciesReference

292662
stoichiometry: 1.0
species: meta i3
type: SpeciesReference

292506
stoichiometry: 1.0
species: meta n2 e7
type: SpeciesReference

293159
stoichiometry: 2.0
species: meta a2
type: SpeciesReference

293000
stoichiometry: 1.0
species: meta n1
type: SpeciesReference

291319
constant: true
units: dimensionless
value: 1.0
type: Parameter

meta i2 e8
initial concentration: 0.01
boundary condition: false
is: C00149
type: Species
name: Mal
is: SBO:0000247
initial amount: NaN
in compartment: 291283
has only substance units: false
is: CHEBI:15589
constant: false

292042
units: dimensionless
value: 25.0
type: LocalParameter

292458
units: dimensionless
value: 3.0
type: LocalParameter

291332
constant: true
units: dimensionless
value: 1.0
type: Parameter

292578
stoichiometry: 1.0
species: meta i1 e8
type: SpeciesReference

292226
stoichiometry: 1.0
species: meta s5 e4
type: SpeciesReference

291760
stoichiometry: 2.0
species: meta s1
type: SpeciesReference

291465
constant: false
units: dimensionless
value: NaN
name: AMP
type: Parameter

292842
stoichiometry: 1.0
species: meta s2 e1
type: SpeciesReference

291747
stoichiometry: 2.0
species: meta a3 e5
type: SpeciesReference

292818
units: dimensionless
value: 0.1
type: LocalParameter

291859
notes: cytoplasmic alpha-glycerophosphate reaction of H-transporter
product: 291908
type: Reaction
is: SBO:0000176
reversible: true
name: v2
kinetic law: 291920
product: 291895
reactant: 291883
reactant: 291871
fast: false

292698
stoichiometry: 1.0
species: meta i2 e8
type: SpeciesReference

292312
stoichiometry: 1.0
species: meta n1
type: SpeciesReference

meta n1
constant: false
boundary condition: true
is: CHEBI:57540
initial concentration: 0.99
has only substance units: false
name: NADm
type: Species
is: C00003
in compartment: 291283
is: SBO:0000247
initial amount: NaN

291944
units: dimensionless
value: 0.1
type: LocalParameter

292275
units: dimensionless
value: 0.003
type: LocalParameter

meta i1 e8
initial amount: NaN
in compartment: 291283
initial concentration: 0.01
type: Species
is: CHEBI:16452
name: Oxa
constant: false
boundary condition: false
has only substance units: false
is: SBO:0000247
is: C00036

291528
constant: false
units: dimensionless
value: NaN
name: CoASAc
type: Parameter

291271
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

291247
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

meta i3
initial concentration: 0.9
is: C00158
boundary condition: true
is: SBO:0000247
has only substance units: false
constant: false
is: CHEBI:16947
initial amount: NaN
in compartment: 291283
name: Cit
type: Species

291871
stoichiometry: 1.0
species: meta s1
type: SpeciesReference

292482
stoichiometry: 1.0
species: meta i2 e8
type: SpeciesReference

293111
units: dimensionless
value: 0.01
type: LocalParameter

meta r2
in compartment: 291283
is: SBO:0000247
is: C00004
initial amount: NaN
type: Species
constant: false
initial concentration: 0.5
name: NADHc
boundary condition: true
is: CHEBI:57945
has only substance units: false

292638
units: dimensionless
value: 5.0
type: LocalParameter

292782
kinetic law: 292806
reactant: 292794
notes: glycolytic intermediate efflux
is: SBO:0000176
fast: false
reversible: true
name: v13
type: Reaction

292926
units: dimensionless
value: 1.0
type: LocalParameter

meta c2 e9
name: CoASAc
initial amount: NaN
type: Species
boundary condition: false
is: CHEBI:57288
is: C00024
initial concentration: 0.01
has only substance units: false
constant: false
is: SBO:0000247
in compartment: 291283

291307
constant: true
units: dimensionless
value: 1.0
type: Parameter

291490
constant: false
units: dimensionless
value: NaN
name: NADHm
type: Parameter

293147
stoichiometry: 1.0
species: meta a1 e5
type: SpeciesReference

292518
stoichiometry: 1.0
species: meta i1 e8
type: SpeciesReference

291809
units: dimensionless
value: 1.0
type: LocalParameter

meta a3 e5
name: ATP
boundary condition: false
is: C00002
is: CHEBI:30616
in compartment: 291283
has only substance units: false
is: SBO:0000247
initial amount: NaN
constant: false
initial concentration: 3.2
type: Species

292963
stoichiometry: 1.0
species: meta n2 e7
type: SpeciesReference

293184
units: dimensionless
value: 100.0
type: LocalParameter

292650
name: v11
reversible: true
product: 292698
is: SBO:0000176
product: 292686
type: Reaction
kinetic law: 292710
fast: false
reactant: 292674
reactant: 292662
notes: Krebs cycle

meta s2 e1
type: Species
is: SBO:0000247
name: aGP
constant: false
has only substance units: false
is: C00093
in compartment: 291283
initial amount: NaN
boundary condition: false
initial concentration: 0.5
is: CHEBI:57597

292566
reversible: true
reactant: 292578
is: SBO:0000176
fast: false
type: Reaction
reactant: 292590
kinetic law: 292626
name: v10
notes: Krebs cycle
product: 292602
product: 292614

293051
units: dimensionless
value: 0.1
type: LocalParameter

292433
stoichiometry: 1.0
species: meta c2 e9
type: SpeciesReference

292030
units: dimensionless
value: 10.0
type: LocalParameter

292178
units: dimensionless
value: 10.0
type: LocalParameter

291847
units: dimensionless
value: 0.1
type: LocalParameter

291453
constant: false
units: dimensionless
value: NaN
name: ATP
type: Parameter

291772
stoichiometry: 2.0
species: meta a2
type: SpeciesReference

292830
kinetic law: 292854
reactant: 292842
notes: alpha-glycerophosphate efflux
is: SBO:0000176
fast: false
reversible: true
name: v14
type: Reaction

292794
stoichiometry: 1.0
species: meta s5 e4
type: SpeciesReference

292214
stoichiometry: 1.0
species: meta r2
type: SpeciesReference

291441
constant: false
units: dimensionless
value: NaN
name: Lac
type: Parameter

292686
stoichiometry: 3.0
species: meta n2 e7
type: SpeciesReference

292890
stoichiometry: 1.0
species: meta a3 e5
type: SpeciesReference

292091
units: dimensionless
value: 0.01
type: LocalParameter

292878
kinetic law: 292914
product: 292902
reactant: 292890
notes: total ATPase reaction
is: SBO:0000176
fast: false
reversible: true
name: v15
type: Reaction

292202
stoichiometry: 1.0
species: meta s4 e3
type: SpeciesReference

meta a1 e5
constant: false
initial amount: NaN
boundary condition: false
in compartment: 291283
type: Species
is: SBO:0000247
is: C00020
initial concentration: 0.4
is: CHEBI:456215
has only substance units: false
name: AMP

meta s5 e4
boundary condition: false
is: C00186
is: CHEBI:16651
type: Species
name: Lac
initial concentration: 0.01
has only substance units: false
initial amount: NaN
is: SBO:0000247
constant: false
in compartment: 291283

292938
units: dimensionless
value: 0.1
type: LocalParameter

292734
kinetic law: 292758
reactant: 292746
notes: glycolytic intermediate efflux
is: SBO:0000176
fast: false
reversible: true
name: v12
type: Reaction

292103
product: 292152
type: Reaction
product: 292140
notes: glycolytic reaction
reversible: true
name: v5
reactant: 292115
kinetic law: 292165
is: SBO:0000176
fast: false
reactant: 292127

292602
stoichiometry: 1.0
species: meta i3
type: SpeciesReference

293063
kinetic law: 293099
product: 293087
reactant: 293075
notes: NADH dehydrogenase
is: SBO:0000176
fast: false
reversible: true
name: v17
type: Reaction

292396
stoichiometry: 1.0
species: meta c1
type: SpeciesReference

292542
units: dimensionless
value: 100.0
type: LocalParameter

293123
reactant: 293147
product: 293159
notes: adenylate kinase
is: SBO:0000176
fast: false
kinetic law: 293172
reversible: true
name: v18
reactant: 293135
type: Reaction

292494
stoichiometry: 1.0
species: meta n1
type: SpeciesReference

291956
type: Reaction
notes: glycolytic reaction
is: SBO:0000176
product: 291994
reactant: 291969
kinetic law: 292018
fast: false
reversible: true
reactant: 291981
product: 292006
name: v3

292263
units: dimensionless
value: 200.0
type: LocalParameter

293196
units: dimensionless
value: 1.0
type: LocalParameter

292951
kinetic law: 293012
type: Reaction
notes: oxidative phosphorylation
is: SBO:0000176
reactant: 292976
name: v16
reversible: true
product: 292988
reactant: 292963
fast: false
product: 293000

292055
kinetic law: 292079
reactant: 292067
notes: glycolytic intermediate efflux
is: SBO:0000176
fast: false
reversible: true
name: v4
type: Reaction

meta c1
name: CoA
in compartment: 291283
is: SBO:0000247
has only substance units: false
is: CHEBI:57287
type: Species
boundary condition: true
is: C00010
initial amount: NaN
initial concentration: 0.95
constant: false

291516
constant: false
units: dimensionless
value: NaN
name: Mal
type: Parameter

292006
stoichiometry: 1.0
species: meta r2
type: SpeciesReference

292866
units: dimensionless
value: 0.5
type: LocalParameter

292902
stoichiometry: 1.0
species: meta a2
type: SpeciesReference

292360
units: dimensionless
value: 25.0
type: LocalParameter

meta s1
in compartment: 291283
name: GAP
type: Species
is: CHEBI:58027
is: C00661
has only substance units: false
initial concentration: 0.1
constant: false
boundary condition: false
initial amount: NaN
is: SBO:0000247

291981
stoichiometry: 1.0
species: meta r1 e6
type: SpeciesReference

292336
stoichiometry: 1.0
species: meta n2 e7
type: SpeciesReference

291822
units: dimensionless
value: 0.003
type: LocalParameter

292140
stoichiometry: 1.0
species: meta s4 e3
type: SpeciesReference

291223
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

291969
stoichiometry: 1.0
species: meta s1
type: SpeciesReference

291392
constant: true
units: dimensionless
value: 0.2
type: Parameter

292770
units: dimensionless
value: 0.1
type: LocalParameter

291429
constant: false
units: dimensionless
value: NaN
name: Pyr
type: Parameter

291356
constant: true
units: dimensionless
value: 0.2
type: Parameter

meta n2 e7
initial amount: NaN
boundary condition: false
type: Species
is: SBO:0000247
is: C00004
has only substance units: false
in compartment: 291283
is: CHEBI:57945
name: NADHm
constant: false
initial concentration: 0.002

292746
stoichiometry: 1.0
species: meta s4 e3
type: SpeciesReference

meta s3 e2
boundary condition: false
in compartment: 291283
constant: false
is: C00236
initial amount: NaN
name: 13DPG
is: SBO:0000247
has only substance units: false
type: Species
is: CHEBI:57604
initial concentration: 0.5

291994
stoichiometry: 1.0
species: meta s3 e2
type: SpeciesReference

292722
units: dimensionless
value: 3.0
type: LocalParameter

meta a2
has only substance units: false
initial amount: NaN
is: C00008
name: ADP
in compartment: 291283
initial concentration: 0.1
is: SBO:0000247
type: Species
is: CHEBI:456216
constant: false
boundary condition: true

meta s4 e3
initial amount: NaN
type: Species
name: Pyr
boundary condition: false
in compartment: 291283
has only substance units: false
constant: false
initial concentration: 0.01
is: C00022
is: SBO:0000247
is: CHEBI:15361

293038
units: dimensionless
value: 0.1
type: LocalParameter

W3 CDTF: Wed Feb 15 00:00:00 GMT 2012

292239
stoichiometry: 1.0
species: meta r1 e6
type: SpeciesReference

292674
stoichiometry: 3.0
species: meta n1
type: SpeciesReference

292590
stoichiometry: 1.0
species: meta c2 e9
type: SpeciesReference

292988
stoichiometry: 3.0
species: meta a3 e5
type: SpeciesReference

292614
stoichiometry: 1.0
species: meta c1
type: SpeciesReference

291295
constant: true
units: dimensionless
value: 1.0
type: Parameter

292421
stoichiometry: 1.0
species: meta n2 e7
type: SpeciesReference

292067
stoichiometry: 1.0
species: meta s3 e2
type: SpeciesReference

292115
stoichiometry: 1.0
species: meta s3 e2
type: SpeciesReference

292384
stoichiometry: 1.0
species: meta s4 e3
type: SpeciesReference

MODEL1202170000
time units: 291235
volume units: 291259
reaction: 292951
units def: 291211
parameter: 291465
species: meta s2 e1
rule: 291723
rule: 291552
species: meta a3 e5
notes: This model is from the article: An old paper revisited: ‘‘A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load’’ by V.V. Dynnik, R. Heinrich and E.E. Sel’kov Nazaret C, Mazat JP. J Theor Biol 2008 Jun;252(3):520-9. 18304584 , Abstract: We revisit an old Russian paper by V.V. Dynnik, R. Heinrich and E.E. Sel’kov (1980a, b) describing: ‘‘A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load’’. We analyse the model mathematically and calculate the control coefficients as a function of ATPase loads. We also evaluate the structure of the metabolic network in terms of elementary flux modes. We show how this model can respond to an ATPase load as well as to the glucose supply. We also show how this simple model can help in understanding the articulation between the major blocks of energetic metabolism, i.e. glycolysis, the Krebs cycle and the H-transporting shuttles. Note: "dynnik_v1.xml": created directly from "heinrich.sci" model file provided by Christine Nazaret IDs changed to as per the paper initial conditions set to steady state results of Fig. 3 may be reproduced by running a a parameter scan over b15 in COPASI "dynnik_v2.xml": rescaled species such as s2_e1 = s2 * e1 are introduced whose evolution may be described through reaction participation, rather than via ODEs original variables are retained as global parameters 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 restr…
species: meta r2
species: meta r1 e6
species: meta a2
parameter: 291307
reaction: 292190
reaction: 291735
reaction: 292055
parameter: 291295
parameter: 291380
parameter: 291332
units def: 291259
parameter: 291417
reaction: 293063
reaction: 292878
rule: 291686
parameter: 291490
parameter: 291356
rule: 291625
is described by: http://identifiers.org/pubmed/18304584
reaction: 292734
species: meta n1
reaction: 292650
is: http://identifiers.org/taxonomy/9606
species: meta a1 e5
area units: area
curated: false
reaction: 292103
rule: 291649
parameter: 291528
compartment: 291283
species: meta s5 e4
reaction: 292566
species: meta i1 e8
parameter: 291368
species: meta i3
parameter: 291453
parameter: 291405
rule: 291661
type: SBMLModel
rule: 291577
species: meta i2 e8
substance units: 291211
reaction: 292372
parameter: 291477
species: meta s3 e2
reaction: 291859
parameter: 291503
reaction: 292470
reaction: 293123
rule: 291601
reaction: 291956
units def: 291235
rule: 291540
rule: 291711
parameter: 291344
reaction: 292830
rule: 291637
parameter: 291441
parameter: 291319
name: Nazaret2008_Dynnik1980_CarbohydrateEnergyMetabolism
rule: 291564
parameter: 291392
reaction: 292782
parameter: 291429
length unit: length
species: meta s4 e3
reaction: 292287
species: meta s1
rule: 291589
species: meta c1

291405
constant: false
units: dimensionless
value: NaN
name: aGP
type: Parameter

293075
stoichiometry: 1.0
species: meta n1
type: SpeciesReference

292554
units: dimensionless
value: 25.0
type: LocalParameter

293135
stoichiometry: 1.0
species: meta a3 e5
type: SpeciesReference

292127
stoichiometry: 2.0
species: meta a2
type: SpeciesReference

291908
stoichiometry: 1.0
species: meta r1 e6
type: SpeciesReference

292409
stoichiometry: 1.0
species: meta n1
type: SpeciesReference

292324
stoichiometry: 1.0
species: meta s1
type: SpeciesReference

292372
reactant: 292396
fast: false
reversible: true
product: 292433
notes: pyruvate dehydrogenase
reactant: 292409
kinetic law: 292446
is: SBO:0000176
name: v8
reactant: 292384
type: Reaction
product: 292421

291735
notes: glycolytic reaction
type: Reaction
product: 291772
product: 291760
modifier: 291784
reversible: true
name: v1
is: SBO:0000176
reactant: 291747
kinetic law: 291796
fast: false

291834
units: dimensionless
value: 0.1
type: LocalParameter

291477
constant: false
units: dimensionless
value: NaN
name: NADc
type: Parameter

meta r1 e6
is: C00003
type: Species
initial amount: NaN
boundary condition: false
initial concentration: 0.1
constant: false
is: CHEBI:57540
name: NADc
is: SBO:0000247
in compartment: 291283
has only substance units: false

292190
reactant: 292214
reactant: 292202
type: Reaction
notes: glycolytic reaction
product: 292239
reversible: true
fast: false
name: v6
product: 292226
kinetic law: 292251
is: SBO:0000176

291344
constant: true
units: dimensionless
value: 4.0
type: Parameter

291895
stoichiometry: 1.0
species: meta s2 e1
type: SpeciesReference

293025
units: dimensionless
value: 5.0
type: LocalParameter

291503
constant: false
units: dimensionless
value: NaN
name: Oxa
type: Parameter

291417
constant: false
units: dimensionless
value: NaN
name: 13DPG
type: Parameter

291380
constant: true
units: dimensionless
value: 0.2
type: Parameter

292152
stoichiometry: 2.0
species: meta a3 e5
type: SpeciesReference

W3 CDTF: Fri May 11 14:05:24 BST 2012

given: Kieran
family: Smallbone

W3 CDTF: Fri May 11 14:05:24 BST 2012

ORG:
  orgname: University of Manchester

orgname: University of Manchester

n:
  given: Kieran
  family: Smallbone

orgname: University of Manchester

ORG:
  orgname: Inistitut Polytechnique Bordeaux
n:
  given: Christine
  family: Nazaret

ORG:
  orgname: Inistitut Polytechnique Bordeaux
n:
  given: Christine
  family: Nazaret

given: Christine
family: Nazaret

given: Kieran
family: Smallbone

orgname: Inistitut Polytechnique Bordeaux

W3 CDTF: Fri Feb 17 11:04:55 GMT 2012