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is: SBO:0000324
constant: true
value: 4.0424
type: Parameter

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reactant: 879218
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: Protein Y mRNA degradation
type: Reaction

metaid_0000106
is: SBO:0000190
constant: true
value: 1.0237
type: Parameter

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is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000060
unit: 878435
name: nM (default)
type: SBMLUnitsDef

metaid_0000073
is: SBO:0000186
constant: true
value: 3.0087
type: Parameter

metaid_0000035
kinetic law: 878868
reactant: 878856
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Cytoplasmic TOC1 degradation
type: Reaction

879110
is: SBO:0000011
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000021
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modifier: 878507
product: 878495
is version of: GO:0006351
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fast: false
reversible: false
name: Light independent LHY transcription
type: Reaction

metaid_0000074
is: SBO:0000190
constant: true
value: 1.0258
type: Parameter

metaid_0000088
is: SBO:0000027
constant: true
value: 0.4033
type: Parameter

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

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is: SBO:0000011
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000022
kinetic law: 878543
reactant: 878531
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: LHY mRNA degradation
type: Reaction

metaid_0000107
is: SBO:0000190
constant: true
value: 3.6064
type: Parameter

metaid_0000036
kinetic law: 878905
product: 878893
reactant: 878880
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: TOC1 movement into nucleus
type: Reaction

metaid_0000121
constant: true
value: 1.0
type: Parameter

metaid_0000085
is: SBO:0000027
constant: true
value: 2.7454
type: Parameter

365384
value: 8.0
type: LocalParameter

879338
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000075
is: SBO:0000363
constant: true
value: 0.036805783
type: Parameter

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

metaid_0000108
is: SBO:0000324
constant: true
value: 4.297
type: Parameter

879350
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stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000023
kinetic law: 878579
modifier: 878567
product: 878555
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: LHY translation
type: Reaction

metaid_0000009
is: SBO:0000278
constant: false
initial concentration: 0.456
boundary condition: false
name: TOC1 mRNA
has only substance units: false
in compartment: metaid_0000005
is version of: C00046
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type: Species
is version of: CHEBI:33699

metaid_0000086
is: SBO:0000324
constant: true
value: 0.0492
type: Parameter

metaid_0000076
is: SBO:0000261
constant: true
value: 0.26593318
type: Parameter

metaid_0000120
is: SBO:0000324
constant: true
value: 1.2
type: Parameter

metaid_0000109
is: SBO:0000027
constant: true
value: 1.7303
type: Parameter

879074
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

878760
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000020
is version of: GO:0006351
reversible: false
kinetic law: 878483
name: LHY transcription by light activation
product: 878459
is version of: GO:0009642
modifier: 878471
type: Reaction
is: SBO:0000183
fast: false

metaid_0000034
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product: 878832
reactant: 878820
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: TOC1 transport out of nucleus
type: Reaction

metaid_0000113
is: SBO:0000324
constant: true
value: 0.1347
type: Parameter

878531
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

metaid_0000045
kinetic law: 879122
product: 879110
reactant: 879098
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: Protein X movement into nucleus
type: Reaction

metaid_0000102
is: SBO:0000186
constant: true
value: 0.0857
type: Parameter

metaid_0000077
is: SBO:0000190
constant: true
value: 1.0258
type: Parameter

metaid_0000008
name: LHY protein in nucleus
in compartment: metaid_0000005
is: O81713
type: Species
is: SBO:0000245
constant: false
has only substance units: false
initial concentration: 0.0855
boundary condition: false
initial amount: NaN

metaid_0000059
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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
type: Reaction

metaid_0000123
constant: true
value: 24.0
type: Parameter

879038
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

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

metaid_0000018
is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.835
initial amount: NaN
in compartment: metaid_0000005
name: light sensitive protein P
type: Species

metaid_0000097
is: SBO:0000324
constant: true
value: 0.2179
type: Parameter

metaid_0000025
kinetic law: 878616
product: 878604
reactant: 878591
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: LHY transport out of nucleus
type: Reaction

metaid_0000112
is: SBO:0000158
constant: true
value: 0.2002
type: Parameter

metaid_0000103
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constant: true
value: 0.1649
type: Parameter

metaid_0000078
is: SBO:0000324
constant: true
value: 3.8231
type: Parameter

metaid_0000122
constant: true
value: 0.0
type: Parameter

878495
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878880
is: SBO:0000010
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species: metaid_0000010
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metaid_0000007
name: LHY protein in cytoplasm
type: Species
is: O81713
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in compartment: metaid_0000005
constant: false

metaid_0000026
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reactant: 878628
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Cytoplasmic LHY degradation
type: Reaction

metaid_0000017
name: Y protein in nucleus
is: SBO:0000245
is version of: GO:0005667
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initial concentration: 0.013
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type: Species

metaid_0000098
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value: 0.6632
type: Parameter

metaid_0000047
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is version of: GO:0030163
is: SBO:0000179
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reversible: false
name: Nuclear Protein X degradation
type: Reaction

metaid_0000089
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value: 0.2431
type: Parameter

metaid_0000111
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constant: true
value: 2.2123
type: Parameter

metaid_0000104
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value: 1.17803247
type: Parameter

879374
is: SBO:0000010
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species: metaid_0000017
type: SpeciesReference

365388
value: 8.0
type: LocalParameter

metaid_0000079
is: SBO:0000027
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value: 2.5734
type: Parameter

878555
is: SBO:0000011
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species: metaid_0000007
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metaid_0000057
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product: 879398
is version of: GO:0006412
is version of: GO:0009642
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fast: false
reversible: false
name: Light dependent production of Protein P
type: Reaction

metaid_0000006
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is: SBO:0000278
constant: false
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in compartment: metaid_0000005
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has only substance units: false
name: LHY mRNA
initial amount: NaN

879314
is: SBO:0000010
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species: metaid_0000016
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metaid_0000099
is: SBO:0000324
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value: 3.3442
type: Parameter

878784
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BIOMD0000000055
units def: metaid_0000004
reaction: metaid_0000050
reaction: metaid_0000031
reaction: metaid_0000030
reaction: metaid_0000025
reaction: metaid_0000045
reaction: metaid_0000026
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is version of: GO:0007623
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parameter: metaid_0000093
parameter: metaid_0000123
curated: true
parameter: metaid_0000110
parameter: metaid_0000087
parameter: metaid_0000117
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reaction: metaid_0000054
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species: metaid_0000011
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length unit: length
type: SBMLModel
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parameter: metaid_0000104
parameter: metaid_0000075
parameter: metaid_0000105
parameter: metaid_0000118
reaction: metaid_0000049
parameter: metaid_0000066
reaction: metaid_0000029
species: metaid_0000006
units def: metaid_0000060
parameter: metaid_0000061
parameter: metaid_0000062
species: metaid_0000014
reaction: metaid_0000041
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reaction: metaid_0000057
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parameter: metaid_0000092
parameter: metaid_0000080
parameter: metaid_0000090
parameter: metaid_0000098
function def: metaid_0000003
parameter: metaid_0000089
reaction: metaid_0000036
species: metaid_0000008
compartment: metaid_0000005
parameter: metaid_0000065
is: ath04710
parameter: metaid_0000085
parameter: metaid_0000115
parameter: metaid_0000086
parameter: metaid_0000116
parameter: metaid_0000077
reaction: metaid_0000023
reaction: metaid_0000020
is: MODEL0737170531
parameter: metaid_0000102
parameter: metaid_0000073
parameter: metaid_0000103
parameter: metaid_0000096
reaction: metaid_0000053
species: metaid_0000012
parameter: metaid_0000083
parameter: metaid_0000113
parameter: metaid_0000084
species: metaid_0000007
species: metaid_0000015
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parameter: metaid_0000100
parameter: metaid_0000071
parameter: metaid_0000101
parameter: metaid_0000091
parameter: metaid_0000121
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
parameter: metaid_0000108
parameter: metaid_0000109

metaid_0000027
kinetic law: 878676
product: 878664
reactant: 878652
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: LHY transport into nucleus
type: Reaction

metaid_0000105
is: SBO:0000261
constant: true
value: 0.064455137
type: Parameter

metaid_0000048
product: 879158
modifier: 879182
is: SBO:0000183
name: Protein Y transcription
type: Reaction
kinetic law: 879206
is version of: GO:0006351
modifier: 879194
reversible: false
modifier: 879170
fast: false

metaid_0000110
is: SBO:0000153
constant: true
value: 0.2485
type: Parameter

metaid_0000124
constant: true
value: 12.0
type: Parameter

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

879050
is: SBO:0000011
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000005
is: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
type: Compartment

878832
is: SBO:0000011
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

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

878459
is: SBO:0000011
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

metaid_0000040
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reactant: 878978
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: Protein X degradation
type: Reaction

878856
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000029
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reactant: 878688
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Nuclear LHY degradation
type: Reaction

metaid_0000093
is: SBO:0000027
constant: true
value: 6.5585
type: Parameter

878447
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

metaid_0000014
type: Species
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boundary condition: false
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name: X protein in nucleus
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constant: false
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878628
is: SBO:0000010
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metaid_0000004
unit: 878447
name: hour (default)
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metaid_0000054
kinetic law: 879362
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reactant: 879338
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: Protein Y into nucleus
type: Reaction

metaid_0000068
is: SBO:0000156
constant: true
value: 0.1687
type: Parameter

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

metaid_0000117
is: SBO:0000153
constant: true
value: 0.5
type: Parameter

metaid_0000094
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constant: true
value: 2.147
type: Parameter

metaid_0000013
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name: X protein in cytoplasm
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879290
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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.
type: FunctionDef

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reactant: 879314
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false
name: Cytoplasmic Protein Y degradation
type: Reaction

879218
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000069
is: SBO:0000324
constant: true
value: 20.44
type: Parameter

metaid_0000067
is: SBO:0000153
constant: true
value: 16.8363
type: Parameter

metaid_0000080
is: SBO:0000153
constant: true
value: 4.324
type: Parameter

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constant: true
value: 1.8066
type: Parameter

metaid_0000095
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constant: true
value: 1.0352
type: Parameter

metaid_0000016
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constant: false
boundary condition: false
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initial concentration: 0.004
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in compartment: metaid_0000005
name: Y protein in cytoplasm
type: Species

878435
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scale: -9
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878712
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constant: true
value: 0.8295
type: Parameter

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constant: true
value: 17.1111
type: Parameter

metaid_0000115
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value: 0.6114
type: Parameter

metaid_0000056
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878978
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species: metaid_0000012
type: SpeciesReference

metaid_0000096
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constant: true
value: 3.3017
type: Parameter

metaid_0000015
initial amount: NaN
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name: Y mRNA
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type: Species
is version of: CHEBI:33699

878893
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879134
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878591
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type: SpeciesReference

metaid_0000114
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value: 1.8258
type: Parameter

metaid_0000101
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value: 2.40178
type: Parameter

metaid_0000065
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value: 1.817
type: Parameter

metaid_0000055
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value: 2.4514
type: Parameter

metaid_0000010
name: TOC1 protein in cytoplasm
is: SBO:0000245
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is: Q9LKL2

879098
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metaid_0000030
name: TOC1 transcription
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metaid_0000044
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is version of: GO:0030163
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name: Cytoplasmic Protein X degradation
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878942
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species: metaid_0000012
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metaid_0000064
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type: Parameter

878604
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metaid_0000050
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reversible: false
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metaid_0000083
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value: 0.0013
type: Parameter

metaid_0000043
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879398
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metaid_0000063
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type: Parameter

metaid_0000070
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type: Parameter

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

878917
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metaid_0000084
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metaid_0000032
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type: Reaction

879158
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species: metaid_0000015
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878688
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metaid_0000012
name: X mRNA
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type: Parameter

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type: Parameter

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type: Parameter

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type: Parameter

metaid_0000071
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type: Parameter

metaid_0000081
is: SBO:0000153
constant: true
value: 0.3166
type: Parameter

metaid_0000052
kinetic law: 879302
product: 879290
reactant: 879278
is version of: GO:0006886
is: SBO:0000185
fast: false
reversible: false
name: Protein Y out of nucleus
type: Reaction

metaid_0000031
kinetic law: 878772
reactant: 878760
is version of: GO:0006402
is: SBO:0000179
fast: false
reversible: false
name: TOC mRNA degradation
type: Reaction

metaid_0000011
name: TOC1 protein in nucleus
constant: false
in compartment: metaid_0000005
has only substance units: false
is: Q9LKL2
initial amount: NaN
initial concentration: 0.4
type: Species
boundary condition: false
is: SBO:0000245

metaid_0000118
is: SBO:0000027
constant: true
value: 1.2
type: Parameter

metaid_0000092
is: SBO:0000324
constant: true
value: 10.1132
type: Parameter

metaid_0000041
kinetic law: 879026
modifier: 879014
product: 879002
is version of: GO:0006412
is: SBO:0000184
fast: false
reversible: false
name: Protein X translation
type: Reaction

878652
is: SBO:0000010
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000061
is: SBO:0000186
constant: true
value: 5.1694
type: Parameter

metaid_0000072
is: SBO:0000027
constant: true
value: 1.2765
type: Parameter

metaid_0000082
is: SBO:0000156
constant: true
value: 2.1509
type: Parameter

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

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