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BIOMD0000000476 - Adams2012 - Locke2006 Circadian Rhythm model refined with Input Signal Light Function

 

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Reference Publication
Publication ID: 22855577
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ.
The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models.
J. Biol. Rhythms 2012 Aug; 27(4): 328-332
  [more]
Model
Original Model: BIOMD0000000476.xml.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1001130000
Submission Date: 13 Jan 2010 15:01:19 UTC
Last Modification Date: 11 Sep 2013 15:39:47 UTC
Creation Date: 20 Feb 2007 13:57:29 UTC
Encoders:  Anthony Hall
   Nick Juty
   Vijayalakshmi Chelliah
   Enuo He
set #1
bqbiol:is Taxonomy Arabidopsis thaliana
bqbiol:isVersionOf Gene Ontology circadian rhythm
set #2
bqmodel:isDerivedFrom BioModels Database Locke2006_CircClock_LL
Notes

As per BIO0000000089.xml but including a functional light.

Model
Publication ID: 22855577 Submission Date: 13 Jan 2010 15:01:19 UTC Last Modification Date: 11 Sep 2013 15:39:47 UTC Creation Date: 20 Feb 2007 13:57:29 UTC
Mathematical expressions
Reactions
cLm transcription cLm degradation cLc translation LHY protein translocation
cLc degradation cLn degradation cTm transcription cTm degradation
Y protein translocation cYn degradation cYc translation cYc degradation
X protein translocation cXc degradation cXc translation cXn degradation
cAc translation PPR7/9 protein translocation cAc degradation cAn degradation
light dependent production of protein P light activation protein P degradation cPn degradation light activation of cAm transcription
light independent cAm transcription cAm degradation cXm transcription cXm degradation
cTc translation TOC1 protein translocation light activation degradation of cTc light independent degradation of cTc
light activation degradation of cTn light independent degradation cTn cYm transcription cYm degradation
Physical entities
Compartments Species
cell LHY mRNA LHY protein in cytoplasm LHY protein in nucleus
TOC1 mRNA TOC1 protein in cytoplasm TOC1 protein in nucleus
X mRNA X protein in cytoplasm X protein in nucleus
Y mRNA Y protein in the cytoplasm Y protein in nucleus
light sensitive protein P PPR7/9 mRNA PPR7/9 protein in cytoplasm
PPR7/9 protein in nucleus    
Global parameters
q1 n0 g0 alpha
n1 a g1 m1
k1 p1 r1 r2
m2 k2 m3 k3
n2 b g2 g3
c m4 k4 p2
r3 r4 m5 m6
k5 m7 m8 k6
n3 d g4 m9
k7 p3 r5 r6
m10 k8 m11 k9
q2 n4 n5 g5
g6 e f m12
k10 p4 r7 r8
m13 k11 m14 k12
p5 k13 m15 q3
q4 g n6 g7
m16 k14 p6 r9
r10 m17 k15 m18
k16 lightAmplitude lightOffset cyclePeriod
photoPeriod phase twilightPeriod  
Reactions (36)
 
 cLm transcription  → [LHY mRNA];   {PPR7/9 protein in nucleus} , {X protein in nucleus} , {light sensitive protein P} , {PPR7/9 protein in nucleus} , {light sensitive protein P} , {X protein in nucleus}
 
 cLm degradation [LHY mRNA] → ;   {LHY mRNA}
 
 cLc translation  → [LHY protein in cytoplasm];   {LHY mRNA} , {LHY mRNA}
 
 LHY protein translocation [LHY protein in cytoplasm] ↔ [LHY protein in nucleus];   {LHY protein in cytoplasm} , {LHY protein in nucleus}
 
 cLc degradation [LHY protein in cytoplasm] → ;   {LHY protein in cytoplasm}
 
 cLn degradation [LHY protein in nucleus] → ;   {LHY protein in nucleus}
 
 cTm transcription  → [TOC1 mRNA];   {Y protein in nucleus} , {LHY protein in nucleus} , {Y protein in nucleus} , {LHY protein in nucleus}
 
 cTm degradation [TOC1 mRNA] → ;   {TOC1 mRNA}
 
 Y protein translocation [Y protein in the cytoplasm] ↔ [Y protein in nucleus];   {Y protein in the cytoplasm} , {Y protein in nucleus}
 
 cYn degradation [Y protein in nucleus] → ;   {Y protein in nucleus}
 
 cYc translation  → [Y protein in the cytoplasm];   {Y mRNA} , {Y mRNA}
 
 cYc degradation [Y protein in the cytoplasm] → ;   {Y protein in the cytoplasm}
 
 X protein translocation [X protein in cytoplasm] ↔ [X protein in nucleus];   {X protein in cytoplasm} , {X protein in nucleus}
 
 cXc degradation [X protein in cytoplasm] → ;   {X protein in cytoplasm}
 
 cXc translation  → [X protein in cytoplasm];   {X mRNA} , {X mRNA}
 
 cXn degradation [X protein in nucleus] → ;   {X protein in nucleus}
 
 cAc translation  → [PPR7/9 protein in cytoplasm];   {PPR7/9 mRNA} , {PPR7/9 mRNA}
 
 PPR7/9 protein translocation [PPR7/9 protein in cytoplasm] ↔ [PPR7/9 protein in nucleus];   {PPR7/9 protein in cytoplasm} , {PPR7/9 protein in nucleus}
 
 cAc degradation [PPR7/9 protein in cytoplasm] → ;   {PPR7/9 protein in cytoplasm}
 
 cAn degradation [PPR7/9 protein in nucleus] → ;   {PPR7/9 protein in nucleus}
 
 light dependent production of protein P  → [light sensitive protein P];  
 
 light activation protein P degradation [light sensitive protein P] → ;   {light sensitive protein P}
 
 cPn degradation [light sensitive protein P] → ;   {light sensitive protein P}
 
 light activation of cAm transcription  → [PPR7/9 mRNA];   {light sensitive protein P} , {light sensitive protein P}
 
 light independent cAm transcription  → [PPR7/9 mRNA];   {LHY protein in nucleus} , {LHY protein in nucleus}
 
 cAm degradation [PPR7/9 mRNA] → ;   {PPR7/9 mRNA}
 
 cXm transcription  → [X mRNA];   {TOC1 protein in nucleus} , {TOC1 protein in nucleus}
 
 cXm degradation [X mRNA] → ;   {X mRNA}
 
 cTc translation  → [TOC1 protein in cytoplasm];   {TOC1 mRNA} , {TOC1 mRNA}
 
 TOC1 protein translocation [TOC1 protein in cytoplasm] ↔ [TOC1 protein in nucleus];   {TOC1 protein in nucleus} , {TOC1 protein in cytoplasm}
 
 light activation degradation of cTc [TOC1 protein in cytoplasm] → ;   {TOC1 protein in cytoplasm}
 
 light independent degradation of cTc [TOC1 protein in cytoplasm] → ;   {TOC1 protein in cytoplasm}
 
 light activation degradation of cTn [TOC1 protein in nucleus] → ;   {TOC1 protein in nucleus}
 
 light independent degradation cTn [TOC1 protein in nucleus] → ;   {TOC1 protein in nucleus}
 
 cYm transcription  → [Y mRNA];   {TOC1 protein in nucleus} , {LHY protein in nucleus} , {light sensitive protein P} , {light sensitive protein P} , {TOC1 protein in nucleus} , {LHY protein in nucleus}
 
 cYm degradation [Y mRNA] → ;   {Y mRNA}
 
Functions (2)
 
 degradation (Michaelis_Menten_Equation) lambda(V, substrate, Km, V*substrate/(Km+substrate))
 
 tanh() light function lambda(t, lightOffset, lightAmplitude, phase, photoPeriod, cyclePeriod, twilightPeriod, lightOffset+0.5*lightAmplitude*(1+tanh(cyclePeriod*((t+phase)/cyclePeriod-floor(floor(t+phase)/cyclePeriod))/twilightPeriod))-0.5*lightAmplitude*(1+tanh((cyclePeriod*((t+phase)/cyclePeriod-floor(floor(t+phase)/cyclePeriod))-photoPeriod)/twilightPeriod))+0.5*lightAmplitude*(1+tanh((cyclePeriod*((t+phase)/cyclePeriod-floor(floor(t+phase)/cyclePeriod))-cyclePeriod)/twilightPeriod)))
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 LHY mRNA
Compartment: cell
Initial concentration: 0.4625
 
 LHY protein in cytoplasm
Compartment: cell
Initial concentration: 0.0132
 
 LHY protein in nucleus
Compartment: cell
Initial concentration: 0.0699
 
 TOC1 mRNA
Compartment: cell
Initial concentration: 0.4303
 
 TOC1 protein in cytoplasm
Compartment: cell
Initial concentration: 10.2965
 
 TOC1 protein in nucleus
Compartment: cell
Initial concentration: 0.5402
 
 X mRNA
Compartment: cell
Initial concentration: 0.0957
 
 X protein in cytoplasm
Compartment: cell
Initial concentration: 1.5413
 
 X protein in nucleus
Compartment: cell
Initial concentration: 0.4585
 
 Y mRNA
Compartment: cell
Initial concentration: 0.0303
 
 Y protein in the cytoplasm
Compartment: cell
Initial concentration: 0.0041
 
 Y protein in nucleus
Compartment: cell
Initial concentration: 0.0122
 
 light sensitive protein P
Compartment: cell
Initial concentration: 0.8476
 
 PPR7/9 mRNA
Compartment: cell
Initial concentration: 14.6921
 
 PPR7/9 protein in cytoplasm
Compartment: cell
Initial concentration: 0.7027
 
 PPR7/9 protein in nucleus
Compartment: cell
Initial concentration: 0.8648
 
Global Parameters (83)
 
 q1
Value: 4.1954
Constant
 
 n0
Value: 0.05
Constant
 
 g0
Value: 1.0
Constant
 
 alpha
Value: 4.0
Constant
 
 n1
Value: 7.8142
Constant
 
 a
Value: 1.2479
Constant
 
 g1
Value: 3.1383
Constant
 
 m1
Value: 1.999
Constant
 
 k1
Value: 2.392
Constant
 
 p1
Value: 0.8295
Constant
 
 r1
Value: 16.8363
Constant
 
 r2
Value: 0.1687
Constant
 
 m2
Value: 20.44
Constant
 
 k2
Value: 1.5644
Constant
 
 m3
Value: 3.6888
Constant
 
 k3
Value: 1.2765
Constant
 
 n2
Value: 3.0087
Constant
 
 b
Value: 1.0258
Constant
 
 g2
Value: 0.0368
Constant
 
 g3
Value: 0.2658
Constant
 
 c
Value: 1.0258
Constant
 
 m4
Value: 3.8231
Constant
 
 k4
Value: 2.5734
Constant
 
 p2
Value: 4.324
Constant
 
 r3
Value: 0.3166
Constant
 
 r4
Value: 2.1509
Constant
 
 m5
Value: 0.0013
Constant
 
 m6
Value: 3.1741
Constant
 
 k5
Value: 2.7454
Constant
 
 m7
Value: 0.0492
Constant
 
 m8
Value: 4.0424
Constant
 
 k6
Value: 0.4033
Constant
 
 n3
Value: 0.2431
Constant
 
 d
Value: 1.4422
Constant
 
 g4
Value: 0.5388
Constant
 
 m9
Value: 10.1132
Constant
 
 k7
Value: 6.5585
Constant
 
 p3
Value: 2.147
Constant
 
 r5
Value: 1.0352
Constant
 
 r6
Value: 3.3017
Constant
 
 m10
Value: 0.2179
Constant
 
 k8
Value: 0.6632
Constant
 
 m11
Value: 3.3442
Constant
 
 k9
Value: 17.1111
Constant
 
 q2
Value: 2.4017
Constant
 
 n4
Value: 0.0857
Constant
 
 n5
Value: 0.1649
Constant
 
 g5
Value: 1.178
Constant
 
 g6
Value: 0.0645
Constant
 
 e
Value: 3.6064
Constant
 
 f
Value: 1.0237
Constant
 
 m12
Value: 4.297
Constant
 
 k10
Value: 1.7303
Constant
 
 p4
Value: 0.2485
Constant
 
 r7
Value: 2.2123
Constant
 
 r8
Value: 0.2002
Constant
 
 m13
Value: 0.1347
Constant
 
 k11
Value: 1.8258
Constant
 
 m14
Value: 0.6114
Constant
 
 k12
Value: 1.8066
Constant
 
 p5
Value: 0.5
Constant
 
 k13
Value: 1.2
Constant
 
 m15
Value: 1.2
Constant
 
 q3
Value: 1.0
Constant
 
 q4
Value: 2.4514
Constant
 
 g
Value: 1.0258
Constant
 
 n6
Value: 8.0706
Constant
 
 g7
Value: 4.0E-4
Constant
 
 m16
Value: 12.2398
Constant
 
 k14
Value: 10.3617
Constant
 
 p6
Value: 0.2907
Constant
 
 r9
Value: 0.2528
Constant
 
 r10
Value: 0.2212
Constant
 
 m17
Value: 4.4505
Constant
 
 k15
Value: 0.0703
Constant
 
 m18
Value: 0.0156
Constant
 
 k16
Value: 0.6104
Constant
 
   lightAmplitude
Value: 1.0
Constant
 
 lightOffset
Constant
 
 cyclePeriod
Value: 24.0
Constant
 
 photoPeriod
Value: 12.0
Constant
 
 phase
Constant
 
 twilightPeriod
Value: 0.0416666667
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000476

Curator's comment: (updated: 09 Sep 2013 15:03:10 BST)

Reporoduces Figure 2b of corresponding publication. 50h simulation, 1000 intervals, using SMBLsimulator 1.1, 'Adams Moulton' solver.

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