metaid_0000062
constant: false
units: metaid_0000045
value: 3.118
name: Qm
type: Parameter

metaid_0000038
is version of: FMA:63194
is: SBO:0000290
constant: true
units: litre
size: 2.0979
spatial dimensions: 3.0
name: Capillary
type: Compartment

926291
stoichiometry: 6.0
species: metaid_0000023
type: SpeciesReference

926315
stoichiometry: 6.0
species: metaid_0000008
type: SpeciesReference

926146
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid_0000024
constant: false
is: CHEBI:16919
name: Cr
boundary condition: false
is: C00300
in compartment: metaid_0000078
is: SBO:0000247
has only substance units: false
type: Species
initial amount: NaN
initial concentration: 1.01056

metaid_0000003
unit: 926110
name: substance
type: SBMLUnitsDef

metaid_0000077
constant: true
units: metaid_0000014
value: 9.199981
name: CTart
type: Parameter

926461
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000095
constant: true
units: metaid_0000004
value: 3.3423645
name: KatpaseVH
type: Parameter

metaid_0000043
constant: false
units: metaid_0000045
value: 12.74981
name: dQMm
type: Parameter

926110
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000105
constant: false
units: dimensionless
value: NaN
name: RStO2m
type: Parameter

metaid_0000057
kinetic law: 926437
is: SBO:0000185
product: 926401
modifier: 926413
modifier: 926425
name: DiffusionTransport
type: Reaction
fast: false
reversible: true
reactant: 926388

926266
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

926242
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

926401
stoichiometry: 1.0
species: metaid_0000071
type: SpeciesReference

metaid_0000097
constant: true
units: metaid_0000045
value: 9.42198
name: dQMmH
type: Parameter

metaid_0000041
is: SBO:0000247
constant: false
initial amount: NaN
name: CFtis
initial concentration: 0.0374
boundary condition: true
has only substance units: false
in compartment: metaid_0000078
type: Species
is version of: CHEBI:15379
is version of: C00007

metaid_0000025
modifier: 926340
kinetic law: 926352
reactant: 926303
product: 926315
is: SBO:0000216
modifier: 926327
reversible: true
fast: false
type: Reaction
name: OxidativePhosphorylation
reactant: 926291
is version of: GO:0006119

metaid_0000042
constant: true
units: metaid_0000045
value: 3.118
name: QWm
type: Parameter

metaid_0000096
constant: true
units: metaid_0000045
value: 7.9167374
name: dQMmM
type: Parameter

metaid_0000082
constant: true
units: metaid_0000014
value: 7800.7
name: KHb
type: Parameter

metaid_0000056
kinetic law: 926376
product: 926364
is: SBO:0000185
fast: false
reversible: true
name: ConvectionTransport
type: Reaction

926158
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000036
unit: 926194
name: min
type: SBMLUnitsDef

metaid_0000074
constant: true
units: metaid_0000060
value: 308.642
name: KMb
type: Parameter

metaid_0000022
reversible: true
is: SBO:0000376
name: ATPase
is version of: http://identifiers.org/ec-code/3.6.1.3
kinetic law: 926278
is version of: GO:0016887
product: 926266
fast: false
reactant: 926254
type: Reaction

metaid_0000019
constant: true
units: dimensionless
value: 2.7
name: nH
type: Parameter

metaid_0000045
unit: 926218
unit: 926206
name: LperMin
type: SBMLUnitsDef

metaid_0000093
constant: true
units: metaid_0000004
value: 1.71080439028658
name: KatpaseM
type: Parameter

926170
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000065
constant: true
units: metaid_0000004
value: 0.3207601
name: KatpaseW
type: Parameter

metaid_0000083
constant: true
units: metaid_0000014
value: 5.18
name: CrbcHb
type: Parameter

metaid_0000063
constant: false
units: metaid_0000045
value: 5338.8
name: PSm
type: Parameter

metaid_0000073
constant: true
units: metaid_0000014
value: 0.5
name: CmcMb
type: Parameter

926254
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000004
unit: 926122
name: perMin
type: SBMLUnitsDef

926230
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000023
type: Species
is: CHEBI:16761
constant: false
initial concentration: 0.001142
has only substance units: false
initial amount: NaN
is: SBO:0000247
name: ADP
is: C00008
boundary condition: false
in compartment: metaid_0000078

metaid_0000018
constant: true
units: metaid_0000014
value: 1.11
name: Kb
type: Parameter

metaid_0000094
constant: true
units: metaid_0000004
value: 2.2581564
name: KatpaseH
type: Parameter

metaid_0000044
constant: false
units: metaid_0000036
value: 0.42
name: tauQm
type: Parameter

metaid_0000064
initial concentration: 5.281527
type: Species
is: SBO:0000247
has version: CHEBI:15379
name: CTcap
has version: C05781
boundary condition: false
has version: C00007
has version: CHEBI:7861
has only substance units: false
initial amount: NaN
has version: GO:0005833
in compartment: metaid_0000038
constant: false

926364
stoichiometry: 1.0
species: metaid_0000064
type: SpeciesReference

metaid_0000084
product: 926485
is: SBO:0000216
fast: false
kinetic law: 926497
is version of: http://identifiers.org/ec-code/2.7.3.2
is version of: GO:0004111
name: CreatineKinase
type: Reaction
is version of: R01881
reactant: 926449
reversible: true
reactant: 926461
product: 926473

metaid_0000053
constant: true
units: metaid_0000014
value: 7.0E-4
name: Km
type: Parameter

metaid_0000109
constant: false
units: metaid_0000005
value: NaN
name: oxygen_phosphorilation_rate_mM
type: Parameter

metaid_0000020
constant: true
units: metaid_0000005
value: 6000.0
name: VfCK
type: Parameter

metaid_0000072
constant: true
units: dimensionless
value: 0.8064
type: Parameter

metaid_0000092
constant: true
units: metaid_0000005
value: 23.11702
name: VmaxVH
type: Parameter

926388
stoichiometry: 1.0
species: metaid_0000064
type: SpeciesReference

926182
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000010
constant: false
units: metaid_0000005
value: 23.11702
name: Vmax
type: Parameter

metaid_0000101
constant: true
units: metaid_0000036
value: 0.42
name: tauQmVH
type: Parameter

926122
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

926485
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

metaid_0000017
constant: true
units: metaid_0000014
value: 3.8
name: Kp
type: Parameter

metaid_0000021
constant: true
units: metaid_0000005
value: 3008.65837589001
name: VrCK
type: Parameter

metaid_0000066
constant: false
units: metaid_0000004
value: 3.3423645
name: KatpaseE
type: Parameter

metaid_0000071
has version: CHEBI:15379
has version: CHEBI:7044
is: SBO:0000247
initial amount: NaN
initial concentration: 0.4084824
has only substance units: false
name: CTtis
boundary condition: false
type: Species
in compartment: metaid_0000078
has version: C00007
has version: C05782
constant: false

BIOMD0000000248
parameter: metaid_0000017
curated: true
length unit: length
parameter: metaid_0000048
rule: metaid_0000106
species: metaid_0000040
units def: metaid_0000036
units def: metaid_0000045
area units: metaid_0000005
parameter: metaid_0000012
species: metaid_0000028
parameter: metaid_0000016
parameter: metaid_0000070
parameter: metaid_0000094
parameter: metaid_0000090
parameter: metaid_0000080
units def: metaid_0000005
name: Lai2007_O2_Transport_Metabolism
species: metaid_0000009
parameter: metaid_0000044
species: metaid_0000041
parameter: metaid_0000098
parameter: metaid_0000088
parameter: metaid_0000077
is described by: http://identifiers.org/pubmed/17380394
parameter: metaid_0000073
parameter: metaid_0000063
parameter: metaid_0000109
rule: metaid_0000075
is: MODEL1004170000
time units: 905439
notes: This file describes the SBML version of the mathematical model in the following journal article: Linking Pulmonary Oxygen Uptake, Muscle Oxygen Utilization and Cellular Metabolism during Exercise, Ann Biomed Eng. 2007 Jun;35(6):956-69. (Pubmed ID: 17380394). This mathematical model simulates oxygen transport and metabolism in skeletal muscle in response to a step change from a warm-up steady state to a higher work rate corresponding to exercise at different levels of intensity: moderate (M), heavy (H) and very heavy (VH). The model parameter values are listed in the tables of this article. The parameter values that are independent of the exercise level are reported in Table 2. The parameter values that depend on the exercise level are reported in Tables 1A, 3 and 4. The model simulations (Figures 2, 3, 4 and 5) were obtained for a representative subject with a set of parameter values different from those in Table 1A, 3 and 4. In the sbml model, these model parameters are used to simulate exercise at a very heavy (VH) intensity for the representative subject. Additionally, the parameter values needed to simulate exercise at moderate (M) and heavy (H) intensity are reported in the list of parameters of the file. The model simulates dynamics of (1) the concentrations of free (F) and total (T) oxygen concentration in blood (CFcap, CTcap) and tissue (CFtis, CTtis), Adenosine Triphosphate (ATP), Adenosine Diphosphate (ADP), Phosphocreatine (PCr) and Creatine (Cr); (2) the metabolic flux of oxidative phosphorylation, creatine kinase and ATPase; (3) the oxygen uptake in blood and oxygen transport rate from blood to tissue during exercise. The simulation also computes muscle oxygen saturation (StO2m) and relative muscle oxygen saturation (RStO2m) in order to compare simulated and experimental responses of human muscle oxygenation during exercise. The model was successfully tested with Roadrunner of the Systems Biology Workbench (SBW). The model simulations obtained with Road…
reaction: metaid_0000057
parameter: metaid_0000021
parameter: metaid_0000011
parameter: metaid_0000015
compartment: metaid_0000038
rule: metaid_0000107
parameter: metaid_0000019
reaction: metaid_0000084
rule: metaid_0000103
reaction: metaid_0000022
is version of: GO:0015671
rule: metaid_0000111
rule: metaid_0000112
reaction: metaid_0000025
rule: metaid_0000102
rule: metaid_0000086
rule: metaid_0000085
parameter: metaid_0000101
parameter: metaid_0000043
parameter: metaid_0000053
units def: metaid_0000004
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parameter: metaid_0000097
parameter: metaid_0000087
compartment: metaid_0000078
units def: metaid_0000060
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parameter: metaid_0000083
parameter: metaid_0000072
parameter: metaid_0000062
parameter: metaid_0000108
species: metaid_0000071
type: SBMLModel
parameter: metaid_0000092
parameter: metaid_0000096
units def: metaid_0000003
rule: metaid_0000076
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parameter: metaid_0000046
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is version of: GO:0072592
reaction: metaid_0000056
parameter: metaid_0000020
parameter: metaid_0000010
parameter: metaid_0000100
parameter: metaid_0000018

metaid_0000087
constant: true
units: dimensionless
value: 81.17123516
name: StO2mW
type: Parameter

metaid_0000091
constant: true
units: metaid_0000005
value: 34.68714
name: VmaxH
type: Parameter

metaid_0000016
constant: true
units: metaid_0000014
value: 3.9
name: Kib
type: Parameter

926206
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000011
constant: true
units: metaid_0000014
value: 0.058
name: Kadp
type: Parameter

metaid_0000046
constant: true
units: metaid_0000045
value: 20000.0
name: PSE
type: Parameter

926449
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

926194
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid_0000080
constant: false
units: dimensionless
value: NaN
name: StO2m
type: Parameter

metaid_0000070
constant: true
units: metaid_0000045
value: 134.2828
name: PSR
type: Parameter

metaid_0000098
constant: true
units: metaid_0000045
value: 12.74981
name: dQMmVH
type: Parameter

metaid_0000069
constant: true
units: metaid_0000045
value: 0.688
name: QRm
type: Parameter

metaid_0000088
constant: true
units: dimensionless
value: 3.0
name: exercise_level
type: Parameter

metaid_0000090
constant: true
units: metaid_0000005
value: 53.5150933
name: VmaxM
type: Parameter

metaid_0000079
constant: true
units: metaid_0000036
value: 3.0
name: tE
type: Parameter

metaid_0000009
constant: false
is: CHEBI:17287
is: C02305
name: PCr
type: Species
is: SBO:0000247
initial concentration: 40.98942
in compartment: metaid_0000078
initial amount: NaN
has only substance units: false
boundary condition: false

metaid_0000060
unit: 926242
unit: 926230
name: permM
type: SBMLUnitsDef

926303
stoichiometry: 1.0
species: metaid_0000071
type: SpeciesReference

metaid_0000012
constant: false
units: metaid_0000004
value: 0.3207601
name: Katpase
type: Parameter

metaid_0000015
constant: true
units: metaid_0000014
value: 3.5
name: Kiq
type: Parameter

metaid_0000040
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in compartment: metaid_0000038
type: Species
initial concentration: 0.03969
is: SBO:0000247
boundary condition: true
has only substance units: false
is version of: CHEBI:15379
name: CFcap
constant: false
is version of: C00007

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exponent: 1.0
scale: -3
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kind: MOLE
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metaid_0000049
constant: true
units: dimensionless
value: 0.45
name: Hct
type: Parameter

metaid_0000108
constant: false
units: metaid_0000005
value: NaN
name: CK_flux_mM
type: Parameter

metaid_0000099
constant: true
units: metaid_0000036
value: 0.32
name: tauQmM
type: Parameter

926473
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000089
constant: false
units: metaid_0000005
value: NaN
name: ATPase_flux_mM
type: Parameter

metaid_0000008
initial amount: NaN
is: C00002
has only substance units: false
constant: false
initial concentration: 8.198857
type: Species
is: SBO:0000247
boundary condition: false
in compartment: metaid_0000078
name: ATP
is: CHEBI:15422

metaid_0000078
is version of: FMA:9641
is: SBO:0000290
constant: true
units: litre
size: 27.8721
spatial dimensions: 3.0
name: Tissue
type: Compartment

metaid_0000013
constant: true
units: metaid_0000014
value: 0.135
name: Kia
type: Parameter

metaid_0000014
unit: 926182
unit: 926170
name: mM
type: SBMLUnitsDef

926218
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid_0000028
initial amount: NaN
is version of: CHEBI:18367
is: SBO:0000247
in compartment: metaid_0000078
type: Species
is version of: C00009
initial concentration: 0.5
has only substance units: false
boundary condition: false
name: Pi
constant: false

metaid_0000100
constant: true
units: metaid_0000036
value: 0.396
name: tauQmH
type: Parameter

metaid_0000048
constant: true
units: metaid_0000045
value: 8.0
name: Qc
type: Parameter

given: Justin
family: Chiou

ORG:
  orgname: Case Western Reserve University
n:
  given: Nicola
  family: Lai

orgname: Case Western Reserve University

W3 CDTF: Fri Oct 16 21:26:03 BST 2009

W3 CDTF: Fri Apr 20 23:18:01 BST 2012