Locke2005_CircadianClock_tanh - PLM_8, version 1

This version is derived from a model from the article: Extension of a genetic network model by iterative experimentation and mathematical analysis. Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ Mol. Syst. Biol. 2005; 1: 2005.0013 16729048,  SBML model of the interlocked feedback loop network The model describes the circuit depicted in Fig. 4 and reproduces the simulations in Figure 5A and 5B. It provides initial conditions, parameter values and rules 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). Compared to the original version in Biomodels database, BIOMD0000000055.xml.origin, this version 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, rather than discrete events in SBML.

Related Publications
Locke J.C.W., Southern M.M., Kozma-Bognar L., Hibberd V., Brown P.E., Turner M.S., Millar A.J. (2005). Extension of a genetic network model by iterative experimentation and mathematical analysis.. Mol. Syst. Biol.. Retrieved from: http://www.nature.com/msb/journal/v1/n1/full/msb4100018.html

Originally submitted to PLaSMo on 2010-05-05 14:54:28

SEEK ID: https://fairdomhub.org/assays/868

Modelling Analysis

BioData SynthSys

Projects: Millar group, PlaSMo model repository

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Locke2005_CircadianClock_tanh - PLM_8

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

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Andrew Millar
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Created: 10th Jan 2019 at 17:41

Last updated: 22nd Jan 2019 at 18:20

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