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notes: Locke2005 - Circadian Clock 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). This model was successfully tested on MathSBML and SBML ODE Solver. Fig 5B is not in the right phase. However, the data is correct relative to the light/dark bars at the top of the figure. This model is described in 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 Molecular Systems Biology [2005; 1: 2005.0013] Abstract: Circadian clocks involve feedback loops that generate rhythmic expression of key genes. Molecular genetic studies in the higher plant Arabidopsis thaliana have revealed a complex clock network. The first part of the network to be identified, a transcriptional feedback loop comprising TIMING OF CAB EXPRESSION 1 (TOC1), LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), fails to account for significant experimental data. We develop an extended model that is based upon a wider range of data and accurately predicts additional experimental results. The model comprises interlocking feedback loops comparable to those identified experimentally in other circadian systems. We propose that each loop receives input signals from light, and that each loop includes a hypothetical component that had not been explicitly identified. Analysis of the model predicted the properties of these components, including an acute light induction at dawn that is rapidly repressed by LHY and CCA1. We fou…
is described by: http://identifiers.org/pubmed/16729048
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notes: Defines light value depending on time of day LD is a function of time of the day, LD=1 at time t=0 (dawn) and changes to LD=1 at time t=12(dusk) and remains at that value until dawn when it resumes it cycle. The original publication made use of a combination of Function definition, rate rules and events to accomplish this while the the model here does the same thing without the use of Events. This makes it portable across simulators without compromising the published model in any way.

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type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000014

metaid_0000038
type: Reaction
kinetic law: 878930
reactant: 878917
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Nuclear TOC1 degradation

878917
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000011

metaid_0000058
type: Reaction
kinetic law: 879434
reactant: 879422
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Protein P degradation

879422
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000018

metaid_0000039
type: Reaction
kinetic law: 878966
modifier: 878954
product: 878942
is version of: GO:0006351
is: SBO:0000183
fast: false
reversible: false
name: Protein X transcription

878942
type: SpeciesReference
is: SBO:0000011
stoichiometry: 1.0
species: metaid_0000012

metaid_0000059
type: Reaction
kinetic law: 879458
reactant: 879446
is version of: GO:0009642
is version of: GO:0045732
is: SBO:0000179
fast: false
reversible: false
name: Light activated Protein P degradation

879446
type: SpeciesReference
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000018

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

ORG:
  orgname: nstitute of Molecular Plant Sciences, University of Edinburgh
n:
  given: Andrew J
  family: Millar

W3 CDTF: Tue May 02 09:15:42 BST 2006

W3 CDTF: Fri Dec 07 17:03:41 GMT 2012