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BIOMD0000000362 - Butenas2004_BloodCoagulation

 

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Reference Publication
Publication ID: 15039440
Butenas S, Orfeo T, Gissel MT, Brummel KE, Mann KG.
The significance of circulating factor IXa in blood.
J. Biol. Chem. 2004 May; 279(22): 22875-22882
Department of Biochemistry, University of Vermont, Burlington, Vermont 05405-0068, USA.  [more]
Model
Original Model: BIOMD0000000362.xml.origin
Submitter: Michael Schubert
Submission ID: MODEL1108260005
Submission Date: 26 Aug 2011 16:15:02 UTC
Last Modification Date: 28 May 2014 16:29:33 UTC
Creation Date: 26 Aug 2011 16:36:52 UTC
Encoders:  Michael Schubert
set #1
bqbiol:isVersionOf Gene Ontology blood coagulation
set #2
bqbiol:hasTaxon Taxonomy Eukaryota
set #3
bqmodel:isDerivedFrom PubMed 8083241
PubMed 9020158
Notes

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 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: 15039440 Submission Date: 26 Aug 2011 16:15:02 UTC Last Modification Date: 28 May 2014 16:29:33 UTC Creation Date: 26 Aug 2011 16:36:52 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
R9 R10 R11 R12
R13 R14 R15 R16
R17 R18 R19 R20
R21 R22 R23 R24
R25 R26 R27 R6b
R8b R12b R18b R28
R29      
Rules
Assignment Rule (variable: IIa+1.2mIIa)      
Physical entities
Compartments Species
compartment_1 TF TF_VII VII
TF_VIIa VIIa Xa
IIa TF_VIIa_X X
TF_VIIa_Xa IX TF_VIIa_IX
IXa II VIII
VIIIa IXa_VIIIa IXa_VIIIa_X
VIIIa1_L VIIIa2 V
Va Xa_Va Xa_Va_II
mIIa TFPI Xa_TFPI
TF_VIIa_Xa_TFPI ATIII Xa_ATIII
mIIa_ATIII IXa_ATIII IIa_ATIII
TF_VIIa_ATIII    
Global parameters
k1 k2 k3 k4
k5 k6 k7 k8
k9 k10 k11 k12
k13 k14 k15 k16
k17 k18 k19 k20
k21 k22 k23 k24
k25 k26 k27 k28
k29 k30 k31 k32
k33 k34 k35 k36
k37 k38 k39 k40
k41 k42 IIa+1.2mIIa k43
k44      
Reactions (33)
 
 R1 [TF] + [VII] ↔ [TF_VII];  
 
 R2 [TF] + [VIIa] ↔ [TF_VIIa];  
 
 R3 [TF_VIIa] + [VII] → [TF_VIIa] + [VIIa];  
 
 R4 [Xa] + [VII] → [Xa] + [VIIa];  
 
 R5 [IIa] + [VII] → [IIa] + [VIIa];  
 
 R6 [TF_VIIa] + [X] ↔ [TF_VIIa_X];  
 
 R7 [TF_VIIa] + [Xa] ↔ [TF_VIIa_Xa];  
 
 R8 [TF_VIIa] + [IX] ↔ [TF_VIIa_IX];  
 
 R9 [Xa] + [II] → [Xa] + [IIa];  
 
 R10 [IIa] + [VIII] → [IIa] + [VIIIa];  
 
 R11 [IXa] + [VIIIa] ↔ [IXa_VIIIa];  
 
 R12 [IXa_VIIIa] + [X] ↔ [IXa_VIIIa_X];  
 
 R13 [VIIIa] ↔ [VIIIa1_L] + [VIIIa2];  
 
 R14 [IXa_VIIIa_X] → [VIIIa1_L] + [VIIIa2] + [X] + [IXa];  
 
 R15 [IXa_VIIIa] → [VIIIa1_L] + [VIIIa2] + [IXa];  
 
 R16 [IIa] + [V] → [IIa] + [Va];  
 
 R17 [Xa] + [Va] ↔ [Xa_Va];  
 
 R18 [Xa_Va] + [II] ↔ [Xa_Va_II];  
 
 R19 [mIIa] + [Xa_Va] → [IIa] + [Xa_Va];  
 
 R20 [Xa] + [TFPI] ↔ [Xa_TFPI];  
 
 R21 [TF_VIIa_Xa] + [TFPI] ↔ [TF_VIIa_Xa_TFPI];  
 
 R22 [TF_VIIa] + [Xa_TFPI] → [TF_VIIa_Xa_TFPI];  
 
 R23 [Xa] + [ATIII] → [Xa_ATIII];  
 
 R24 [mIIa] + [ATIII] → [mIIa_ATIII];  
 
 R25 [IXa] + [ATIII] → [IXa_ATIII];  
 
 R26 [IIa] + [ATIII] → [IIa_ATIII];  
 
 R27 [TF_VIIa] + [ATIII] → [TF_VIIa_ATIII];  
 
 R6b [TF_VIIa_X] → [TF_VIIa_Xa];  
 
 R8b [TF_VIIa_IX] → [TF_VIIa] + [IXa];  
 
 R12b [IXa_VIIIa_X] → [IXa_VIIIa] + [Xa];  
 
 R18b [Xa_Va_II] → [Xa_Va] + [mIIa];  
 
 R28 [IXa] + [X] → [IXa] + [Xa];  
 
 R29 [mIIa] + [V] → [mIIa] + [Va];  
 
Rules (1)
 
 Assignment Rule (name: IIa_plus_1_2mIIa) IIa+1.2mIIa = IIa+1.2*mIIa
 
   compartment_1 Spatial dimensions: 3.0  Compartment size: 1.0
 
 TF
Compartment: compartment_1
Initial concentration: 0.0
 
 TF_VII
Compartment: compartment_1
Initial concentration: 0.0
 
 VII
Compartment: compartment_1
Initial concentration: 1.0E-8
 
 TF_VIIa
Compartment: compartment_1
Initial concentration: 0.0
 
 VIIa
Compartment: compartment_1
Initial concentration: 1.0E-10
 
 Xa
Compartment: compartment_1
Initial concentration: 9.4E-11
 
 IIa
Compartment: compartment_1
Initial concentration: 1.0E-9
 
 TF_VIIa_X
Compartment: compartment_1
Initial concentration: 0.0
 
 X
Compartment: compartment_1
Initial concentration: 1.6E-7
 
 TF_VIIa_Xa
Compartment: compartment_1
Initial concentration: 0.0
 
 IX
Compartment: compartment_1
Initial concentration: 9.0E-8
 
 TF_VIIa_IX
Compartment: compartment_1
Initial concentration: 0.0
 
 IXa
Compartment: compartment_1
Initial concentration: 2.1E-10
 
 II
Compartment: compartment_1
Initial concentration: 1.4E-6
 
 VIII
Compartment: compartment_1
Initial concentration: 7.0E-10
 
 VIIIa
Compartment: compartment_1
Initial concentration: 0.0
 
 IXa_VIIIa
Compartment: compartment_1
Initial concentration: 0.0
 
 IXa_VIIIa_X
Compartment: compartment_1
Initial concentration: 0.0
 
 VIIIa1_L
Compartment: compartment_1
Initial concentration: 0.0
 
 VIIIa2
Compartment: compartment_1
Initial concentration: 0.0
 
 V
Compartment: compartment_1
Initial concentration: 2.0E-8
 
 Va
Compartment: compartment_1
Initial concentration: 0.0
 
 Xa_Va
Compartment: compartment_1
Initial concentration: 0.0
 
 Xa_Va_II
Compartment: compartment_1
Initial concentration: 0.0
 
 mIIa
Compartment: compartment_1
Initial concentration: 0.0
 
 TFPI
Compartment: compartment_1
Initial concentration: 2.5E-9
 
 Xa_TFPI
Compartment: compartment_1
Initial concentration: 0.0
 
 TF_VIIa_Xa_TFPI
Compartment: compartment_1
Initial concentration: 0.0
 
 ATIII
Compartment: compartment_1
Initial concentration: 3.4E-6
 
 Xa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
 mIIa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
 IXa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
 IIa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
 TF_VIIa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
Global Parameters (45)
 
 k1
Value: 0.0031
Constant
 
 k2
Value: 3200000.0
Constant
 
 k3
Value: 0.0031
Constant
 
 k4
Value: 2.3E7
Constant
 
 k5
Value: 440000.0
Constant
 
 k6
Value: 1.3E7
Constant
 
 k7
Value: 23000.0
Constant
 
 k8
Value: 1.05
Constant
 
 k9
Value: 2.5E7
Constant
 
 k10
Value: 6.0
Constant
 
 k11
Value: 19.0
Constant
 
 k12
Value: 2.2E7
Constant
 
 k13
Value: 2.4
Constant
 
 k14
Value: 1.0E7
Constant
 
 k15
Value: 1.8
Constant
 
 k16
Value: 7500.0
Constant
 
 k17
Value: 2.0E7
Constant
 
 k18
Value: 0.0050
Constant
 
 k19
Value: 1.0E7
Constant
 
 k20
Value: 0.0010
Constant
 
 k21
Value: 1.0E8
Constant
 
 k22
Value: 8.2
Constant
 
 k23
Value: 22000.0
Constant
 
 k24
Value: 0.0060
Constant
 
 k25
Value: 0.0010
Constant
 
 k26
Value: 2.0E7
Constant
 
 k27
Value: 0.2
Constant
 
 k28
Value: 4.0E8
Constant
 
 k29
Value: 103.0
Constant
 
 k30
Value: 1.0E8
Constant
 
 k31
Value: 63.5
Constant
 
 k32
Value: 1.5E7
Constant
 
 k33
Value: 3.6E-4
Constant
 
 k34
Value: 900000.0
Constant
 
 k35
Value: 1.1E-4
Constant
 
 k36
Value: 3.2E8
Constant
 
 k37
Value: 5.0E7
Constant
 
 k38
Value: 1500.0
Constant
 
 k39
Value: 7100.0
Constant
 
 k40
Value: 490.0
Constant
 
 k41
Value: 7100.0
Constant
 
 k42
Value: 230.0
Constant
 
   IIa+1.2mIIa
Value: 1.0E-9
 
 k43
Value: 5700.0
Constant
 
 k44
Value: 3000000.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000362

Curator's comment: (updated: 26 Aug 2011 17:26:19 BST)

Reproduction of figure 1 of the article.

Model integrated using PySCeS and plotted with Matplotlib.

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