This a model from the article:
Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana.
Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ Mol. Syst. Biol.2006;Volume:2;Page:59 17102804,
Abstract:
Our computational model of the circadian clock comprised the feedback loop between LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and TIMING OF CAB EXPRESSION 1 (TOC1), and a predicted, interlocking feedback loop involving TOC1 and a hypothetical component Y. Experiments based on model predictions suggested GIGANTEA (GI) as a candidate for Y. We now extend the model to include a recently demonstrated feedback loop between the TOC1 homologues PSEUDO-RESPONSE REGULATOR 7 (PRR7), PRR9 and LHY and CCA1. This three-loop network explains the rhythmic phenotype of toc1 mutant alleles. Model predictions fit closely to new data on the gi;lhy;cca1 mutant, which confirm that GI is a major contributor to Y function. Analysis of the three-loop network suggests that the plant clock consists of morning and evening oscillators, coupled intracellularly, which may be analogous to coupled, morning and evening clock cells in Drosophila and the mouse.


The model describes a three loops model of the Arabidopsis circadian clock. It provides initial conditions, parameter values and reactions for the production rates of the following species: LHY mRNA (cLm), cytoplasmic LHY (cLc), nuclear LHY (cLn), TOC1 mRNA (cTm), cytoplasmic TOC1 (cTc), nuclear TOC1 (cTn), X mRNA (cXm), cytoplasmic X (cXc), nuclear X (cXn), Y mRNA (cYm), cytoplasmic Y (cYc), nuclear Y (cYn), nuclear P (cPn), APRR7/9 mRNA, cytoplasmic APRR7/9, and nuclear APRR7/9.

The paper describes the behaviour of the model in constant light (LL) and day-night cycle (LD). However, the current model only contains the LL cycle. Some parameter values should be changed from the wild-type (WT) ones in order to simulate the effect of mutations. These changes are listed in the notes of relevant parameters.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

V substrate Km V substrate Km substrate t offset amplitude phase pulseDuration cyclePeriod rampDuration offset 0.5 amplitude 1 cyclePeriod t phase cyclePeriod t phase cyclePeriod rampDuration 0.5 amplitude 1 cyclePeriod t phase cyclePeriod t phase cyclePeriod pulseDuration rampDuration 0.5 amplitude 1 cyclePeriod t phase cyclePeriod t phase cyclePeriod cyclePeriod rampDuration

In lhy;cca1 mutation plan p1'=0.001*p1=0.8295e-3

In toc1 mutation plant p2'=0.001*p2=4.324e-3

In gi mutation plant p4'=30%*p4=0.3*0.2485=0.07455

In ppr7;prr9 mutation plant p6'=0.001*p6=0.2907e-3.

light=1 when light is present,0 otherwise.

step1 stepFunction t offsetStep1 amplitudeStep1 phaseStep1 pulseDurationStep1 cyclePeriodStep1 rampDurationStep1 a 5 a 1 alpha 5 alpha 1 b 5 b 1 c 5 c 1 d 5 d 1 e 5 e 1 f 5 f 1 g 5 g 1 g7 0.4 g7 0 m5 1.3 m5 0 m7 49.2 m7 0 light 10 light 0 compartment g0 alpha g0 alpha cAn alpha light q1 cPn n0 n1 cXn a g1 a cXn a compartment function_1 m1 cLm k1 compartment p1 cLm compartment r1 cLc r2 cLn compartment function_1 m2 cLc k2 compartment function_1 m3 cLn k3 compartment n2 cYn b g2 b cYn b g3 c g3 c cLn c compartment function_1 m4 cTm k4 compartment r7 cYc r8 cYn compartment function_1 m14 cYn k12 compartment p4 cYm compartment function_1 m13 cYc k11 compartment r5 cXc r6 cXn compartment function_1 m10 cXc k8 compartment p3 cXm compartment function_1 m11 cXn k9 compartment p6 cAm compartment r9 cAc r10 cAn compartment function_1 m17 cAc k15 compartment function_1 m18 cAn k16 1 light p5 compartment q3 light cPn compartment compartment m15 cPn k13 cPn light q4 cPn compartment compartment n6 cLn g g7 g cLn g compartment m16 cAm k14 cAm compartment n3 cTn d g4 d cTn d compartment m9 cXm k7 cXm p2 compartment cTm compartment r4 cTn r3 cTc compartment 1 light m5 cTc k5 cTc m6 compartment cTc k5 cTc compartment 1 light m7 cTn k6 cTn m8 compartment cTn k6 cTn compartment light q2 cPn light n4 n5 g5 e g5 e cTn e g6 f g6 f cLn f compartment m12 cYm k10 cYm