Hansen2019 - Nine species reduced model of blood coagulation

  public model
Model Identifier
BIOMD0000000755
Short description 
its a nine species reduced model of Hockin 2002. Model uses different level of reduction (5,7,9,11) and testing the best alignment with Hockin model results
Format
SBML (L2V4)
Related Publication
  • Automated reduction of blood coagulation models.
  • Hansen KB, Shadden SC
  • International journal for numerical methods in biomedical engineering , 6/ 2019 , pages: e3220 , PubMed ID: 31161687
  • Department of Mechanical Engineering, University of California Berkeley, Berkeley, California, United States.
  • Mathematical modeling of thrombosis typically involves modeling the coagulation cascade. Models of coagulation generally involve the reaction kinetics for dozens of proteins. The resulting system of equations is difficult to parameterize and its numerical solution is challenging when coupled to blood flow or other physics important to clotting. Prior research suggests that essential aspects of coagulation may be reproduced by simpler models. This evidence motivates a systematic approach to model reduction. We herein introduce an automated framework to generate reduced-order models of blood coagulation. The framework consists of nested optimizations, where an outer optimization selects the optimal species for the reduced-order model and an inner optimization selects the optimal reaction rates for the new coagulation network. The framework was tested on an established 34-species coagulation model to rigorously consider what level of model fidelity is necessary to capture essential coagulation dynamics. The results indicate that a nine-species reduced-order model is sufficient to reproduce the thrombin dynamics of the benchmark 34-species model for a range of tissue factor concentrations, including those not included in the optimization process. Further model reduction begins to compromise the ability to capture the thrombin generation process. The framework proposed herein enables automated development of reduced-order models of coagulation that maintain essential dynamics used to model thrombosis.
Contributors
Submitter of the first revision: Krishna Kumar Tiwari
Submitter of this revision: Krishna Kumar Tiwari
Modellers: Krishna Kumar Tiwari

Metadata information

is (2 statements)
BioModels Database MODEL1907180004
BioModels Database BIOMD0000000755

isDescribedBy (1 statement)
PubMed 31161687

hasTaxon (1 statement)
Taxonomy Homo sapiens

hasProperty (2 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Gene Ontology blood coagulation

unknownQualifier (1 statement)
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Curated
Modelling approach(es)
ordinary differential equation model
Tags

Connected external resources

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Name Description Size Actions

Model files
Hansen2019.xml SBML L2V4 file for the curated model 37.81 KB Preview | Download

Additional files
Hansen2019.cps COPASI 4.30 (Build240) file for the curated model. 65.29 KB Preview | Download
Hansen2019.sedml SEDML file for the curated model 3.17 KB Preview | Download

  • Model originally submitted by : Krishna Kumar Tiwari
  • Submitted: Jul 18, 2019 4:48:53 PM
  • Last Modified: Apr 8, 2021 9:38:34 AM
Revisions
  • Version: 5 public model Download this version
    • Submitted on: Apr 8, 2021 9:38:34 AM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Automatically added model identifier BIOMD0000000755
  • Version: 4 public model Download this version
    • Submitted on: Mar 29, 2021 10:38:41 AM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Updated model file with missing annotations.
  • Version: 3 public model Download this version
    • Submitted on: Jul 18, 2019 4:48:53 PM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Automatically added model identifier BIOMD0000000755

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
mIIa

Prothrombin 		0.0 mol
Xa Va

Coagulation factor V ; Coagulation factor X ; Active 		0.0 mol
Xa Va II

Prothrombin ; Coagulation factor V ; Coagulation factor X 		0.0 mol
TF

Tissue factor 		1.0E-9 mol
II

Prothrombin 		1.4E-6 mol
IIa

Prothrombin ; Active 		0.0 mol
X

Coagulation factor X 		1.6E-7 mol
Reactions
Reactions Rate Parameters
Xa_Va_II => Xa_Va + mIIa compartment*k1*Xa_Va_II k1=77540.2
Xa_Va + II => Xa_Va_II compartment*k1*Xa_Va*II k1=2.56984E12
TF + X => Xa_Va compartment*k1*TF*X k1=121.267
Xa_Va + mIIa => Xa_Va + IIa compartment*k1*Xa_Va*mIIa k1=6.96794E10
TF + X + II => TF + X + IIa compartment*k1*TF*X*II k1=4.74645E-16
Curator's comment:
(added: 18 Jul 2019, 16:48:01, updated: 18 Jul 2019, 16:48:01)
Data created using COPASI 4.24 (build197) using different doses of TF (as per Literature). Graph created using Microsoft excel. Plotted y axis is in mole where as in literature, its plotted as nM. Y axis in both are similar considering mol to nmol conversion.