Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO.
Methods Mol Biol
; 1158: 337-58, 2014.
Article
en En
| MEDLINE
| ID: mdl-24792063
ABSTRACT
Circadian clocks are endogenous timekeepers that produce oscillations with a period of about one day. Their rhythmicity originates from complex gene regulatory networks at the cellular level. In the last decades, computational models have been proven to be a powerful tool in order to understand the dynamics and design principles of the complex regulatory circuitries underlying the circadian clocks of different organisms. We present the process of model development using a small and simplified two-gene regulatory network of the Arabidopsis circadian clock. Subsequently, we discuss important numerical techniques to analyze such a mathematical model using XPP-AUTO. We show how to solve deterministic and stochastic ordinary differential equations and how to compute bifurcation diagrams or simulate phase-shift experiments. We finally discuss the contributions of modeling to the understanding and dissection of the Arabidopsis circadian system.
Texto completo:
1
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Arabidopsis
/
Relojes Circadianos
/
Modelos Biológicos
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2014
Tipo del documento:
Article