Cazzaniga2014 - Blood Coagulation with Platelet Activation
Model Identifier
MODEL1807180003
Short description
Mathematical model of blood coagulation with platelet activation. Model includes factor XII, factor VIIIa fragments, meizothrombin, kallikrein, C1-inhibitor, alpha1-Antitrypsin, alpha2-Antiplasmin, fibrinogen and fibrillin.
Format
SBML
(L2V4)
Related Publication
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Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization
- Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri
- BioMed Research International , 6/ 2014 , Volume 2014 , DOI: 10.1155/2014/863298
- Dipartimento di Scienze Umane e Sociali, Universit`a degli Studi di Bergamo, 24129 Bergamo, Italy. SYSBIO Centre for Systems Biology, 20126 Milano, Italy. Istituto di Analisi dei Sistemi ed Informatica “Antonio Ruberti”, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
- The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.
Contributors
Submitter of the first revision: Matthew Roberts
Submitter of this revision: Matthew Roberts
Modellers: Matthew Roberts
Submitter of this revision: Matthew Roberts
Modellers: Matthew Roberts
Metadata information
isVersionOf (1 statement)
hasPart (1 statement)
isDescribedBy (1 statement)
hasPart (1 statement)
isDescribedBy (1 statement)
Curation status
Non-curated
Tags
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
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Model files |
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| Cazzaniga2014.xml | SBML L2V4 representation of Cazzaniga2014 - Blood Coagulation with Platelet Activation | 207.37 KB | Preview | Download |
Additional files |
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| Cazzaniga2014.cps | Model COPASI file. Reactions and kinetic rates given in table 1. Initial conditions given in table 2. Simulation only worked using the values in tables 1 and 2 to reproduce figure 2 (unable to reproduce figures 6,7,8,10 and 11) using COPASI 4.22 (Buid 170) and 4.23 (Build 184). | 350.76 KB | Preview | Download |
| fig2.png | Simulated IIa peak off by 2e-7 M. Clotting time approximately 15s too soon. | 15.09 KB | Preview | Download |
- Model originally submitted by : Matthew Roberts
- Submitted: Jul 18, 2018 11:43:59 AM
- Last Modified: Jul 18, 2018 11:43:59 AM
Revisions
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Version: 2
- Submitted on: Jul 18, 2018 11:43:59 AM
- Submitted by: Matthew Roberts
- With comment: Edited model metadata online.