Hansen2019 - Seven species reduced model of blood coagulation

  public model
Model Identifier
MODEL1907180003
Short description
its a seven 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

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

Curation status
Non-curated
Modelling approach(es)
ordinary differential equation model
Tags

Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files
reduced_seven_species.xml SBML file of the model Version 2 Level 1 17.10 KB Preview | Download

Additional files
reduced_seven_species.cps COPASI 4.24 (build 197) file for the model 47.69 KB Preview | Download
reduced_seven_species.sedml SEDML file for the model 13.83 KB Preview | Download

  • Model originally submitted by : Krishna Kumar Tiwari
  • Submitted: Jul 18, 2019 4:32:23 PM
  • Last Modified: Jul 18, 2019 4:32:23 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Jul 18, 2019 4:32:23 PM
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Edited model metadata online.