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39
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47
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10
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040927
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040805
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28
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21
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52
is: SBO:0000035
constant: true
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name: k14
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38
kinetic law: 041590
modifier: 041578
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reversible: false
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46
constant: true
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040733
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041047
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18
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040634
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11
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041360
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041180
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59
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8
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initial amount: NaN
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boundary condition: false
type: Species
name: VIIIa_IXa

27
kinetic law: 040999
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040538
is: SBO:0000010
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species: 1
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32
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product: 041252
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041348
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species: 7
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41
is: SBO:0000036
constant: true
value: 1.0E7
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51
is: SBO:0000035
constant: true
value: 8.2
name: k13
type: Parameter

49
is: SBO:0000035
constant: true
value: 0.3
name: k11
type: Parameter

61
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment_1
type: Compartment

041529
is: SBO:0000461
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species: 17
type: SpeciesReference

040975
is: SBO:0000461
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species: 7
type: SpeciesReference

12
is: P00451
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.0E-10
initial amount: NaN
in compartment: 61
name: VIII
type: Species

041264
is: SBO:0000011
stoichiometry: 1.0
species: 14
type: SpeciesReference

041420
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stoichiometry: 1.0
species: 11
type: SpeciesReference

9
name: X_VIIIa_IXa
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constant: false
has only substance units: false
initial concentration: 0.0
type: Species
has part: P00740
has part: P00742
has part: P00451
boundary condition: false
in compartment: 61

33
kinetic law: 041324
product: 041312
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reactant: 041288
fast: false
reversible: true
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type: Reaction

40
is: SBO:0000036
constant: true
value: 2.0E7
name: k2
type: Parameter

50
is: SBO:0000035
constant: true
value: 1.15
name: k12
type: Parameter

26
kinetic law: 040939
product: 040927
product: 040914
reactant: 040902
reactant: 040890
fast: false
reversible: false
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type: Reaction

041204
is: SBO:0000011
stoichiometry: 1.0
species: 18
type: SpeciesReference

040684
is: SBO:0000010
stoichiometry: 1.0
species: 6
type: SpeciesReference

48
is: SBO:0000038
constant: true
value: 0.4
name: k10
type: Parameter

041132
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species: 15
type: SpeciesReference

040745
is: SBO:0000010
stoichiometry: 1.0
species: 8
type: SpeciesReference

60
constant: false
value: 0.0
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type: Parameter

13
is version of: P00451
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
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name: VIIIa
type: Species

58
constant: true
value: 0.02
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type: Parameter

041035
is: SBO:0000461
stoichiometry: 1.0
species: 14
type: SpeciesReference

24
kinetic law: 040817
product: 040805
product: 040793
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type: Reaction

1
is: P00740
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.0E-8
initial amount: NaN
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name: IX
type: Species

040963
is: SBO:0000461
stoichiometry: 1.0
species: 7
type: SpeciesReference

34
kinetic law: 041372
product: 041360
reactant: 041348
reactant: 041336
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reversible: true
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6
type: Species
in compartment: 61
has part: P13726
boundary condition: false
has only substance units: false
has part: P00742
initial amount: NaN
constant: false
initial concentration: 0.0
name: X_TF_VIIa

041565
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040829
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040586
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species: 2
type: SpeciesReference

57
is: SBO:0000038
constant: true
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name: k19
type: Parameter

041469
is: SBO:0000461
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species: 18
type: SpeciesReference

43
is: SBO:0000036
constant: true
value: 1.0E7
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041396
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species: 18
type: SpeciesReference

041336
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041156
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species: 16
type: SpeciesReference

15
is: P00734
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.4E-6
initial amount: NaN
in compartment: 61
name: II
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041095
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species: 14
type: SpeciesReference

041408
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species: 18
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25
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product: 040865
product: 040853
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reversible: false
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type: Reaction

041083
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species: 14
type: SpeciesReference

14
is version of: P00734
constant: false
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initial concentration: 0.0
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name: IIa
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040659
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040610
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040757
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35
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product: 041408
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reactant: 041384
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reversible: false
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type: Reaction

7
is version of: P00742
constant: false
boundary condition: false
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initial concentration: 0.0
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name: Xa
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041481
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species: 13
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56
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041288
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040914
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42
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040550
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041300
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22
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3
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4
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name: IXa
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36
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040865
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55
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45
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17
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BIOMD0000000336
reaction: 27
type: SBMLModel
parameter: 46
notes: This model is from the article: A model for the tissue factor pathway to thrombin. II. A mathematical simulation. Jones KC, Mann KG. J Biol Chem. 1994 Sep 16;269(37):23367-73. 8083242 , Abstract: A mathematical simulation of the tissue factor pathway to the generation of thrombin has been developed using a combination of empirical, estimated, and deduced rate constants for reactions involving the activation of factor IX, X, V, and VIII, in the formation of thrombin, as well as rate constants for the assembly of the coagulation enzyme complexes which involve factor VIIIa-factor IXa (intrinsic tenase) and factor Va-Xa (prothrombinase) assembled on phospholipid membrane. Differential equations describing the fate of each species in the reaction were developed and solved using an interactive procedure based upon the Runge-Kutta technique. In addition to the theoretical considerations involving the reactions of the tissue factor pathway, a physical constraint associated with the stability of the factor VIIIa-factor IXa complex has been incorporated into the model based upon the empirical observations associated with the stability of this complex. The model system provides a realistic accounting of the fates of each of the proteins in the coagulation reaction through a range of initiator (factor VIIa-tissue factor) concentrations ranging from 5 pM to 5 nM. The model is responsive to alterations in the concentrations of factor VIII, factor V, and their respective activated species, factor VIIIa and factor Va, and overall provides a reasonable approximation of empirical data. The computer model permits the assessment of the reaction over a broad range of conditions and provides a useful tool for the development and management of reaction studies. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use . To cite Bi…
parameter: 51
is described by: http://identifiers.org/pubmed/8083242
parameter: 49
created:
  W3 CDTF: Mon Jun 06 18:21:19 BST 2011
species: 3
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parameter: 57
parameter: 42
function def: 62
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is version of: GO:0007596
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parameter: 45
rule: 63
reaction: 38
reaction: 36
time units: 858180
reaction: 24
reaction: 26
reaction: 29
species: 15
parameter: 50
parameter: 48
compartment: 61
parameter: 53
curated: true
occurs in: http://identifiers.org/taxonomy/2759
parameter: 41
reaction: 32
length unit: length
substance units: metaid_0000254
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reaction: 20
species: 11
species: 10
parameter: 56
creator:
  ORG:
    orgname: EBI
  n:
    given: Michael
    family: Schubert
parameter: 39
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is: MODEL1106060000
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species: 2
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parameter: 52
species: 8
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parameter: 40
parameter: 43
reaction: 34
species: 7
name: Jones1994_BloodCoagulation
area units: area
reaction: 37
reaction: 22
species: 13
reaction: 19
species: 12
species: 4
parameter: 58
name: function_4_VIIIa_IXa_degradation_2
species: 18
reaction: 25

5
is: P00742
constant: false
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initial concentration: 1.7E-7
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in compartment: 61
name: X
type: Species

2
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name: IX_TF_VIIa

23
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040853
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54
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041011
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040697
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040793
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041228
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species: 18
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16
initial concentration: 0.0
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has part: P00742

44
is: SBO:0000036
constant: true
value: 1.0E8
name: k6
type: Parameter

W3 CDTF: Fri Apr 20 22:53:01 BST 2012