Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO

Schmal C, Leloup J-C, Gonze D (2014)
In: Plant Circadian Networks. Staiger D (Ed); Methods in Molecular Biology, 1158. Berlin: Springer: 337-358.

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Staiger, Dorothee
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.
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Schmal C, Leloup J-C, Gonze D. Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. In: Staiger D, ed. Plant Circadian Networks. Methods in Molecular Biology. Vol 1158. Berlin: Springer; 2014: 337-358.
Schmal, C., Leloup, J. - C., & Gonze, D. (2014). Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. In D. Staiger (Ed.), Methods in Molecular Biology: Vol. 1158. Plant Circadian Networks (pp. 337-358). Berlin: Springer.
Schmal, C., Leloup, J. - C., and Gonze, D. (2014). “Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO” in Plant Circadian Networks, ed. D. Staiger Methods in Molecular Biology, vol. 1158, (Berlin: Springer), 337-358.
Schmal, C., Leloup, J.-C., & Gonze, D., 2014. Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. In D. Staiger, ed. Plant Circadian Networks. Methods in Molecular Biology. no.1158 Berlin: Springer, pp. 337-358.
C. Schmal, J.-C. Leloup, and D. Gonze, “Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO”, Plant Circadian Networks, D. Staiger, ed., Methods in Molecular Biology, vol. 1158, Berlin: Springer, 2014, pp.337-358.
Schmal, C., Leloup, J.-C., Gonze, D.: Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO. In: Staiger, D. (ed.) Plant Circadian Networks. Methods in Molecular Biology. 1158, p. 337-358. Springer, Berlin (2014).
Schmal, Christoph, Leloup, Jean-Christophe, and Gonze, Didier. “Modeling and simulating the Arabidopsis thaliana circadian clock using XPP-AUTO”. Plant Circadian Networks. Ed. Dorothee Staiger. Berlin: Springer, 2014.Vol. 1158. Methods in Molecular Biology. 337-358.
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A Compact Model for the Complex Plant Circadian Clock.
De Caluwe J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D., Front Plant Sci 7(), 2016
PMID: 26904049

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