Name
Abstract | ||
|---|---|---|
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing multi-scale models for instance. While singular perturbation theory is a standard mathematical tool to analyze the different time scales of a dynamical system and decompose the system accordingly, tropical methods provide a simple algebraic framework to perform these analyses systematically in polynomial systems. The crux of these methods is in the computation of tropical equilibrations. In this paper we show that constraint-based methods, using reified constraints for expressing the equilibration conditions, make it possible to numerically solve non-linear tropical equilibration problems, out of reach of standard computation methods. We illustrate this approach first with the detailed reduction of a simple biochemical mechanism, the Michaelis-Menten enzymatic reaction model, and second, with large-scale performance figures obtained on the http://biomodels.net repository. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1186/s13015-014-0024-2 | Algorithms for Molecular Biology |
Keywords | Field | DocType |
algorithms,biomedical research,bioinformatics | Algebraic number,Polynomial,Computer science,Constraint programming,Systems biology,Singular perturbation,Dynamical systems theory,Bioinformatics,Dynamical system,Computation | Journal |
Volume | Issue | ISSN |
9 | 1 | 1748-7188 |
Citations | PageRank | References |
0 | 0.34 | 10 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Sylvain Soliman | 1 | 484 | 35.02 |
| François Fages | 2 | 0 | 0.68 |
| Ovidiu Radulescu | 3 | 0 | 0.68 |