Gulati2014 - Simplified model of fibrinogen recovery following brown snake bite_1

  public model
Model Identifier
MODEL1805090001
Short description 
Bridging systems biology and pharmacokinetics–pharmacodynamics has resulted in models that are highly complex and complicated. They usually contain large numbers of states and parameters and describe multiple input–output relationships. Based on any given data set relating to a specific input–output process, it is possible that some states of the system are either less important or have no influence at all. In this study, we explore a simplification of a systems pharmacology model of the coagulation network for use in describing the time course of fibrinogen recovery after a brown snake bite. The technique of proper lumping is used to simplify the 62-state systems model to a 5-state model that describes the brown snake venom–fibrinogen relationship while maintaining an appropriate mechanistic relationship. The simplified 5-state model explains the observed decline and recovery in fibrinogen concentrations well. The techniques used in this study can be applied to other multiscale models.
Format
SBML (L2V4)
Related Publication
  • Scale reduction of a systems coagulation model with an application to modeling pharmacokinetic-pharmacodynamic data.
  • Gulati A, Isbister GK, Duffull SB
  • CPT: Pharmacometrics & Systems Pharmacology , 1/ 2014 , Volume 3 , pages: e90 , PubMed ID: 24402117
  • School of Pharmacy, University of Otago, Dunedin, New Zealand. Department of Clinical Toxicology and Pharmacology, Calvary Mater Newcastle, New South Wales, Australia. Discipline of Clinical Pharmacology, University of Newcastle, New South Wales, Australia.
  • Bridging systems biology and pharmacokinetics-pharmacodynamics has resulted in models that are highly complex and complicated. They usually contain large numbers of states and parameters and describe multiple input-output relationships. Based on any given data set relating to a specific input-output process, it is possible that some states of the system are either less important or have no influence at all. In this study, we explore a simplification of a systems pharmacology model of the coagulation network for use in describing the time course of fibrinogen recovery after a brown snake bite. The technique of proper lumping is used to simplify the 62-state systems model to a 5-state model that describes the brown snake venom-fibrinogen relationship while maintaining an appropriate mechanistic relationship. The simplified 5-state model explains the observed decline and recovery in fibrinogen concentrations well. The techniques used in this study can be applied to other multiscale models.
Contributors
Submitter of the first revision: Matthew Roberts
Submitter of this revision: Ahmad Zyoud
Modellers: Tung Nguyen, Matthew Roberts, Ahmad Zyoud

Metadata information

is (1 statement)
BioModels Database MODEL1805090001

isDescribedBy (1 statement)
PubMed 24402117

isDerivedFrom (1 statement)
PubMed 19516255

hasProperty (4 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Gene Ontology coagulation
Gene Ontology fibrinogen complex
UBERON snake venom

occursIn (1 statement)
Brenda Tissue Ontology blood

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

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Model files
Gulati2014.xml SBML L2V4 representation of Gulati2014 - Simplified model of fibrinogen recovery following brown snake bite 48.67 KB Preview | Download

Additional files
Gulati2014.cps COPASI version 4.27 (Build 217) representation of Gulati2014 - Simplified model of fibrinogen recovery following brown snake bite 87.43 KB Preview | Download
Gulati2014.sedml sed-ml L1V2 representation of Gulati2014 - Simplified model of fibrinogen recovery following brown snake bite 1.78 KB Preview | Download

  • Model originally submitted by : Matthew Roberts
  • Submitted: May 21, 2018 4:00:35 PM
  • Last Modified: Apr 30, 2020 5:56:37 PM
Revisions
  • Version: 15 public model Download this version
    • Submitted on: Apr 30, 2020 5:56:37 PM
    • Submitted by: Ahmad Zyoud
    • With comment: Automatically added model identifier
  • Version: 13 public model Download this version
    • Submitted on: Apr 30, 2020 5:01:23 PM
    • Submitted by: Tung Nguyen
    • With comment: Automatically added model identifier
  • Version: 10 public model Download this version
    • Submitted on: Apr 30, 2020 4:29:55 PM
    • Submitted by: Ahmad Zyoud
    • With comment: Automatically added model identifier
  • Version: 8 public model Download this version
    • Submitted on: Apr 30, 2020 3:04:41 PM
    • Submitted by: Tung Nguyen
    • With comment: Automatically added model identifier
  • Version: 7 public model Download this version
    • Submitted on: Apr 30, 2020 2:40:41 PM
    • Submitted by: Ahmad Zyoud
    • With comment: Automatically added model identifier
  • Version: 5 public model Download this version
    • Submitted on: Apr 30, 2020 10:12:47 AM
    • Submitted by: Ahmad Zyoud
    • With comment: Automatically added model identifier
  • Version: 3 public model Download this version
    • Submitted on: May 21, 2018 4:00:35 PM
    • Submitted by: Matthew Roberts
    • With comment: Uploaded COPASI file and curated figure (not a perfect reproduction) to facilitate the curation process in the future

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Curator's comment:
(added: 30 Apr 2020, 10:12:26, updated: 30 Apr 2020, 10:12:26)
Figure 2C has been reproduced using Copasi 4.27 (Build 217) The unit of the y-axis has been converted from nmol/L into g/L