Locke2006_CircadianClock_tanh - PLM_10, version 1

This is a version derived from a model from the article: <strong>Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. </strong> Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ <em>Mol. Syst. Biol.</em>2006;Volume:2;Page:59 <a href="http://www.ncbi.nlm.nih.gov/pubmed/17102804">17102804</a>,  

The model describes a three loop circuit 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 cycles (LD). The version curated on Biomodels had no LD input, allowing only simulation in LL conditions<strong>:</strong> <a href="http://www.ebi.ac.uk/biomodels/models-main/publ/BIOMD0000000089.xml.origin"><i>BIOMD0000000089.xml.origin</i></a>.

The version uploaded here uses a better description of the light-dark cycle, by Drs. Ozgur Akman and Kevin Stratford. The model contains a candidate for a community-standard cyclic function, which uses tanh functions to achieve rapid yet numerically continuous steps from light to darkness. The SBML file was validated by CSBE, including by Dr. Richard Adams.

Related Publications
Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ (2006). Extension of a genetic network model by iterative experimentation and mathematical analysis.. Mol. Syst. Biol.. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/16729048

Originally submitted to PLaSMo on 2010-05-12 17:38:15

SEEK ID: https://fairdomhub.org/assays/869

Modelling Analysis

BioData SynthSys

Projects: Millar group, PlaSMo model repository

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Locke2006_CircadianClock_tanh - PLM_10

Assay position:

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

help Creators and Submitter
Additional credit

Andrew Millar


Views: 1215

Created: 10th Jan 2019 at 17:41

Last updated: 22nd Jan 2019 at 18:20

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