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BIOMD0000000412 - Pokhilko2012_CircClock_RepressilatorFeedbackloop

 

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Reference Publication
Publication ID: 22395476
Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ.
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.
Mol. Syst. Biol. 2012; 8: 574
School of Biological Sciences, University of Edinburgh, Edinburgh, UK.  [more]
Model
Original Model: BIOMD0000000412.xml.origin
Submitter: Alexandra Pokhilko
Submission ID: MODEL1109200000
Submission Date: 20 Sep 2011 13:12:46 UTC
Last Modification Date: 12 Feb 2013 15:40:34 UTC
Creation Date: 18 Aug 2011 14:47:18 UTC
Encoders:  Vijayalakshmi Chelliah
   Alexandra Pokhilko
set #1
bqbiol:isVersionOf Gene Ontology circadian rhythm
set #2
bqbiol:occursIn Taxonomy Arabidopsis thaliana
Notes

This model is from the article:
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops
Pokhilko A, Fernández AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ. Mol Syst Biol. 2012 Mar 6;8:574. 22395476 ,
Abstract:
Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene PSEUDO-RESPONSE REGULATOR 9 was repressed by an evening gene, previously identified with TIMING OF CAB EXPRESSION1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure.

Model
Publication ID: 22395476 Submission Date: 20 Sep 2011 13:12:46 UTC Last Modification Date: 12 Feb 2013 15:40:34 UTC Creation Date: 18 Aug 2011 14:47:18 UTC
Mathematical expressions
Reactions
cL_m_trscr cL_m_degr cL_trsl cL_degr
cL_modif cLm_degr cP_trsl cP_degr
cP9_m_trscr cP9_m_degr cP9_trsl cP9_degr
cP7_m_trscr cP7_m_degr cP7_trsl cP7_degr
cNI_m_trscr cNI_m_degr cNI_trsl cNI_degr
cT_m_trscr cT_m_degr cT_trsl cT_degr
cE4_m_trscr cE4_m_degr cE4_trsl cE4_degr
cE3_m_trscr cE3_m_degr cE3_trsl cE3_degr
cE3n_import cE3n_degr cLUX_m_trscr cLUX_m_degr
cLUX_trsl cLUX_degr cCOP1c_trsl cCOP1c_degr
cCOP1n_import cCOP1n_degr cCOP1d_activ cCOP1d_degr
cG_m_trscr cG_m_degr cG_trsl cG_degr
cG_cZTL_assoc cZTL_trsl cZTL_degr cZG_degr
cG_cE3_assoc cEG_degr cEC_form cEC_degr
Physical entities
Compartments Species
default      
def cCOP1c cCOP1d cCOP1n
cE3 cE3_m cE3n
cE4 cE4_m cEC
cEG cG cG_m
cL cLUX cLUX_m
cL_m cLm cNI
cNI_m cP cP7
cP7_m cP9 cP9_m
cT cT_m cZG
cZTL s1 s2
s3 s4 s5
s6 s7 s8
s9 s10 s11
s12 s13 s14
s15 s16 s17
s18 s19 s20
s21 s22 s23
s24 s25 s26
s27 s28 s29
s30 s31 s32
s33 s34 s35
s36 s37 s38
s39 s40 s41
s42 s43 s44
s45 s46 s47
s48 s49 s50
s51    
Global parameters
n1 n2 n3 n4
n5 n6 n7 n8
n9 n10 n11 n12
n13 n14 g1 g2
g3 g4 g5 g6
g7 g8 g9 g10
g11 g12 g13 g14
g15 g16 m1 m2
m3 m4 m5 m6
m7 m8 m9 m10
m11 m12 m13 m14
m15 m16 m17 m18
m19 m20 m21 m22
m23 m24 m25 m26
m27 m28 m29 m30
m31 m32 m33 m34
m35 m36 m37 m38
m39 a b c
d e f p1
p2 p3 p4 p5
p6 p7 p8 p9
p10 p11 p12 p13
p14 p15 p16 p17
p18 p19 p20 p21
p22 p23 p24 p25
p26 p27 p28 p29
p30 p31 q1 q2
q3 L D E34
Gn EGn lightOffset cyclePeriod
lightAmplitude phase twilightPeriod photoPeriod
Reactions (56)
 
 cL_m_trscr [s1] → [cL_m];   {cNI} , {cP} , {cP7} , {cP9} , {cT}
 
 cL_m_degr [cL_m] → [s2];  
 
 cL_trsl [s3] → [cL];   {cL_m}
 
 cL_degr [cL] → [s4];  
 
 cL_modif [s5] → [cLm];   {cL}
 
 cLm_degr [cLm] → [s6];  
 
 cP_trsl [s7] → [cP];  
 
 cP_degr [cP] → [s8];  
 
 cP9_m_trscr [s9] → [cP9_m];   {cEC} , {cL} , {cP}
 
 cP9_m_degr [cP9_m] → [s10];  
 
 cP9_trsl [s11] → [cP9];   {cP9_m}
 
 cP9_degr [cP9] → [s12];  
 
 cP7_m_trscr [s13] → [cP7_m];   {cL} , {cLm} , {cP9}
 
 cP7_m_degr [cP7_m] → [s14];  
 
 cP7_trsl [s15] → [cP7];   {cP7_m}
 
 cP7_degr [cP7] → [s16];  
 
 cNI_m_trscr [s17] → [cNI_m];   {cLm} , {cP7}
 
 cNI_m_degr [cNI_m] → [s18];  
 
 cNI_trsl [s19] → [cNI];   {cNI_m}
 
 cNI_degr [cNI] → [s20];  
 
 cT_m_trscr [s21] → [cT_m];   {cEC} , {cL}
 
 cT_m_degr [cT_m] → [s22];  
 
 cT_trsl [s23] → [cT];   {cT_m}
 
 cT_degr [cT] → [s24];   {cZG} , {cZTL}
 
 cE4_m_trscr [s25] → [cE4_m];   {cEC} , {cL}
 
 cE4_m_degr [cE4_m] → [s26];  
 
 cE4_trsl [s27] → [cE4];   {cE4_m}
 
 cE4_degr [cE4] → [s28];   {cCOP1d} , {cCOP1n} , {cE3n} , {cLUX}
 
 cE3_m_trscr [s29] → [cE3_m];   {cL}
 
 cE3_m_degr [cE3_m] → [s30];  
 
 cE3_trsl [s31] → [cE3];   {cE3_m}
 
 cE3_degr [cE3] → [s32];   {cCOP1c}
 
 cE3n_import [cE3] → [cE3n];  
 
 cE3n_degr [cE3n] → [s33];   {cCOP1d} , {cCOP1n} , {cE4} , {cG} , {cLUX}
 
 cLUX_m_trscr [s34] → [cLUX_m];   {cEC} , {cL}
 
 cLUX_m_degr [cLUX_m] → [s35];  
 
 cLUX_trsl [s36] → [cLUX];   {cLUX_m}
 
 cLUX_degr [cLUX] → [s37];   {cCOP1d} , {cCOP1n} , {cE3n} , {cE4}
 
 cCOP1c_trsl [s38] → [cCOP1c];  
 
 cCOP1c_degr [cCOP1c] → [s39];  
 
 cCOP1n_import [cCOP1c] → [cCOP1n];  
 
 cCOP1n_degr [cCOP1n] → [s40];  
 
 cCOP1d_activ [cCOP1n] → [cCOP1d];   {cP}
 
 cCOP1d_degr [cCOP1d] → [s41];  
 
 cG_m_trscr [s42] → [cG_m];   {cEC} , {cL} , {cP}
 
 cG_m_degr [cG_m] → [s43];  
 
 cG_trsl [s44] → [cG];   {cG_m}
 
 cG_degr [cG] → [s45];   {cE3n}
 
 cG_cZTL_assoc [cG] + [cZTL] ↔ [cZG];  
 
 cZTL_trsl [s46] → [cZTL];  
 
 cZTL_degr [cZTL] → [s47];  
 
 cZG_degr [cZG] → [s48];  
 
 cG_cE3_assoc [cE3] + [cG] → [cEG];  
 
 cEG_degr [cEG] → [s49];   {cCOP1c} , {cCOP1d} , {cCOP1n} , {cE3n} , {cG}
 
 cEC_form [s50] → [cEC];   {cCOP1d} , {cCOP1n} , {cE3n} , {cE4} , {cLUX}
 
 cEC_degr [cEC] → [s51];   {cCOP1d} , {cCOP1n} , {cE3n} , {cEG} , {cG}
 
Functions (57)
 
 function_4_cLUX_m_trscr lambda(cEC, cL, def, e, g2, g6, n13, n13*g2/(cEC+g2)*g6^e/(cL^e+g6^e)/def)
 
 function_4_cL_m_trscr lambda(L, a, cNI, cP, cP7, cP9, cT, def, g1, n1, q1, (L*q1*cP+n1*g1^a/((cP9+cP7+cNI+cT)^a+g1^a))/def)
 
 function_4_cL_trsl lambda(L, cL_m, def, p1, p2, cL_m*(p1*L+p2)/def)
 
 function_4_cL_m_degr lambda(D, L, cL_m, def, m1, m2, (m1*L+m2*D)*cL_m/def)
 
 function_4_cL_degr lambda(c, cL, def, g3, m3, p3, (m3*cL+p3*cL^c/(cL^c+g3^c))/def)
 
 function_4_cL_modif lambda(c, cL, def, g3, p3, p3*cL^c/(cL^c+g3^c)/def)
 
 function_4_cLm_degr lambda(cLm, def, m4, m4*cLm/def)
 
 function_4_cP_trsl lambda(L, cP, def, p7, p7*(1-L)*(1-cP)/def)
 
 function_4_cP9_m_trscr_1 lambda(L, cEC, cL, cP, def, e, g8, g9, n4, n7, q3, (L*q3*cP+(n4+n7*cL^e/(cL^e+g9^e))*g8/(cEC+g8))/def)
 
 function_4_cP_degr lambda(L, cP, def, m11, m11*cP*L/def)
 
 function_4_cP9_m_degr lambda(cP9_m, def, m12, m12*cP9_m/def)
 
 function_4_cP9_trsl lambda(cP9_m, def, p8, p8*cP9_m/def)
 
 function_4_cP9_degr lambda(D, cP9, def, m13, m22, (m13+m22*D)*cP9/def)
 
 function_4_cP7_m_trscr lambda(cL, cLm, cP9, def, e, f, g10, g11, n8, n9, (n8*(cLm+cL)^e/((cLm+cL)^e+g10^e)+n9*cP9^f/(cP9^f+g11^f))/def)
 
 function_4_cP7_m_degr lambda(cP7_m, def, m14, m14*cP7_m/def)
 
 function_4_cP7_trsl lambda(cP7_m, def, p9, p9*cP7_m/def)
 
 function_4_cP7_degr lambda(D, cP7, def, m15, m23, (m15+m23*D)*cP7/def)
 
 function_4_cCOP1c_degr lambda(L, cCOP1c, def, m27, p15, m27*cCOP1c*(1+p15*L)/def)
 
 function_4_cCOP1n_import lambda(cCOP1c, def, p6, p6*cCOP1c/def)
 
 function_4_cCOP1d_activ lambda(L, cCOP1n, cP, def, n14, n6, (n6*L*cP*cCOP1n+n14*cCOP1n)/def)
 
 function_4_cCOP1d_degr lambda(D, cCOP1d, def, m31, m33, m31*(1+m33*D)*cCOP1d/def)
 
 function_4_cCOP1n_degr lambda(L, cCOP1n, def, m27, p15, m27*cCOP1n*(1+p15*L)/def)
 
 function_4_cG_m_trscr_1 lambda(L, cEC, cL, cP, def, e, g14, g15, n12, q2, (L*q2*cP+n12*g14/(cEC+g14)*g15^e/(cL^e+g15^e))/def)
 
 function_4_cG_m_degr lambda(cG_m, def, m18, m18*cG_m/def)
 
 function_4_cG_trsl lambda(cG_m, def, p11, p11*cG_m/def)
 
 function_4_cG_degr lambda(cE3n, cG, def, m19, p17, p28, p29, (m19*cG+p28*cG-p29*p28*cG/(p29+m19+p17*cE3n))/def)
 
 function_4_cG_cZTL_assoc lambda(D, L, cG, cZG, cZTL, def, p12, p13, (p12*L*cZTL*cG-p13*D*cZG)/def)
 
 function_4_cZTL_trsl lambda(def, p14, p14/def)
 
 function_4_cZG_degr lambda(cZG, def, m21, m21*cZG/def)
 
 function_4_cZTL_degr lambda(cZTL, def, m20, m20*cZTL/def)
 
 function_4_cG_cE3_assoc lambda(cE3, cG, def, p17, p17*cE3*cG/def)
 
 function_4_cNI_m_trscr lambda(b, cLm, cP7, def, e, g12, g13, n10, n11, (n10*cLm^e/(cLm^e+g12^e)+n11*cP7^b/(cP7^b+g13^b))/def)
 
 function_4_cNI_m_degr lambda(cNI_m, def, m16, m16*cNI_m/def)
 
 function_4_cNI_trsl lambda(cNI_m, def, p10, p10*cNI_m/def)
 
 function_4_cNI_degr lambda(D, cNI, def, m17, m24, (m17+m24*D)*cNI/def)
 
 function_4_cT_m_trscr_1 lambda(cEC, cL, def, e, g4, g5, n2, n2*g4/(cEC+g4)*g5^e/(cL^e+g5^e)/def)
 
 function_4_cT_m_degr lambda(cT_m, def, m5, m5*cT_m/def)
 
 function_4_cT_trsl lambda(cT_m, def, p4, p4*cT_m/def)
 
 function_4_cT_degr lambda(D, cT, cZG, cZTL, def, m6, m7, m8, p5, ((m6+m7*D)*cT*(p5*cZTL+cZG)+m8*cT)/def)
 
 function_4_cE4_m_degr lambda(cE4_m, def, m34, m34*cE4_m/def)
 
 function_4_cE4_trsl lambda(cE4_m, def, p23, p23*cE4_m/def)
 
 function_4_cE4_degr lambda(cCOP1d, cCOP1n, cE3n, cE4, cLUX, def, m35, m36, m37, p21, p25, p26, (m35*cE4+p25*cE4*cE3n-p21*p25*cE4*cE3n/(p26*cLUX+p21+m37*cCOP1d+m36*cCOP1n))/def)
 
 function_4_cE3_m_trscr lambda(cL, def, e, g16, n3, n3*g16^e/(cL^e+g16^e)/def)
 
 function_4_cE3_trsl lambda(cE3_m, def, p16, p16*cE3_m/def)
 
 function_4_cE3_m_degr lambda(cE3_m, def, m26, m26*cE3_m/def)
 
 function_4_cE3_degr lambda(cCOP1c, cE3, def, m9, m9*cE3*cCOP1c/def)
 
 function_4_cE3n_import lambda(cE3, cE3n, def, p19, p20, (p19*cE3-p20*cE3n)/def)
 
 function_4_cE3n_degr lambda(cCOP1d, cCOP1n, cE3n, cE4, cG, cLUX, def, m19, m29, m30, m36, m37, p17, p21, p25, p26, p28, p29, (m29*cE3n*cCOP1n+m30*cE3n*cCOP1d+p25*cE4*cE3n-p21*p25*cE4*cE3n/(p26*cLUX+p21+m37*cCOP1d+m36*cCOP1n)+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/def)
 
 function_4_cLUX_m_degr lambda(cLUX_m, def, m34, m34*cLUX_m/def)
 
 function_4_cLUX_trsl lambda(cLUX_m, def, p27, p27*cLUX_m/def)
 
 function_4_cLUX_degr lambda(cCOP1d, cCOP1n, cE3n, cE4, cLUX, def, m36, m37, m39, p21, p25, p26, (m39*cLUX+p26*cLUX*p25*cE4*cE3n/(p26*cLUX+p21+m37*cCOP1d+m36*cCOP1n))/def)
 
 function_4_cCOP1c_trsl lambda(def, n5, n5/def)
 
 function_4_cEG_degr lambda(cCOP1c, cCOP1d, cCOP1n, cE3n, cEG, cG, def, m10, m19, m9, p17, p18, p28, p29, p31, (m9*cEG*cCOP1c+p18*cEG-p31*(p18*cEG+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/(m9*cCOP1n+m10*cCOP1d+p31))/def)
 
 function_4_cEC_form lambda(cCOP1d, cCOP1n, cE3n, cE4, cLUX, def, m36, m37, p21, p25, p26, p26*cLUX*p25*cE4*cE3n/(p26*cLUX+p21+m37*cCOP1d+m36*cCOP1n)/def)
 
 function_4_cEC_degr lambda(L, cCOP1d, cCOP1n, cE3n, cEC, cEG, cG, d, def, g7, m10, m19, m32, m36, m37, m9, p17, p18, p24, p28, p29, p31, (m36*cCOP1n*cEC+m37*cCOP1d*cEC+m32*cEC*(1+p24*L*(p28*cG/(p29+m19+p17*cE3n)+(p18*cEG+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/(m9*cCOP1n+m10*cCOP1d+p31))^d/((p28*cG/(p29+m19+p17*cE3n)+(p18*cEG+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/(m9*cCOP1n+m10*cCOP1d+p31))^d+g7^d)))/def)
 
 function_4_cE4_m_trscr_1 lambda(cEC, cL, def, e, g2, g6, n13, n13*g2/(cEC+g2)*g6^e/(cL^e+g6^e)/def)
 
 LightFunction lambda(t, lightOffset, lightAmplitude, cyclePeriod, photoPeriod, phase, 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)))
 
  Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 def Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 cCOP1c
Compartment: def
Initial concentration: 0.3269
 
 cCOP1d
Compartment: def
Initial concentration: 0.2566
 
 cCOP1n
Compartment: def
Initial concentration: 0.65
 
 cE3
Compartment: def
Initial concentration: 0.1503
 
 cE3_m
Compartment: def
Initial concentration: 0.2991
 
 cE3n
Compartment: def
Initial concentration: 0.0286
 
 cE4
Compartment: def
Initial concentration: 0.207
 
 cE4_m
Compartment: def
Initial concentration: 0.1012
 
 cEC
Compartment: def
Initial concentration: 0.0709
 
 cEG
Compartment: def
Initial concentration: 0.0041
 
 cG
Compartment: def
Initial concentration: 0.0196
 
 cG_m
Compartment: def
Initial concentration: 0.1017
 
 cL
Compartment: def
Initial concentration: 0.506
 
 cLUX
Compartment: def
Initial concentration: 0.576
 
 cLUX_m
Compartment: def
Initial concentration: 0.1012
 
 cL_m
Compartment: def
Initial concentration: 1.0151
 
 cLm
Compartment: def
Initial concentration: 0.0788
 
 cNI
Compartment: def
Initial concentration: 0.0697
 
 cNI_m
Compartment: def
Initial concentration: 0.0731
 
 cP
Compartment: def
Initial concentration: 0.956
 
 cP7
Compartment: def
Initial concentration: 0.1167
 
 cP7_m
Compartment: def
Initial concentration: 0.4016
 
 cP9
Compartment: def
Initial concentration: 0.0238
 
 cP9_m
Compartment: def
Initial concentration: 0.0658
 
 cT
Compartment: def
Initial concentration: 0.0435
 
 cT_m
Compartment: def
Initial concentration: 0.0977
 
 cZG
Compartment: def
Initial concentration: 0.0755
 
 cZTL
Compartment: def
Initial concentration: 0.2505
 
 s1
Compartment: def
Initial amount: 0.0
 
 s2
Compartment: def
Initial amount: 0.0
 
 s3
Compartment: def
Initial amount: 0.0
 
 s4
Compartment: def
Initial amount: 0.0
 
 s5
Compartment: def
Initial amount: 0.0
 
 s6
Compartment: def
Initial amount: 0.0
 
 s7
Compartment: def
Initial amount: 0.0
 
 s8
Compartment: def
Initial amount: 0.0
 
 s9
Compartment: def
Initial amount: 0.0
 
 s10
Compartment: def
Initial amount: 0.0
 
 s11
Compartment: def
Initial amount: 0.0
 
 s12
Compartment: def
Initial amount: 0.0
 
 s13
Compartment: def
Initial amount: 0.0
 
 s14
Compartment: def
Initial amount: 0.0
 
 s15
Compartment: def
Initial amount: 0.0
 
 s16
Compartment: def
Initial amount: 0.0
 
 s17
Compartment: def
Initial amount: 0.0
 
 s18
Compartment: def
Initial amount: 0.0
 
 s19
Compartment: def
Initial amount: 0.0
 
 s20
Compartment: def
Initial amount: 0.0
 
 s21
Compartment: def
Initial amount: 0.0
 
 s22
Compartment: def
Initial amount: 0.0
 
 s23
Compartment: def
Initial amount: 0.0
 
 s24
Compartment: def
Initial amount: 0.0
 
 s25
Compartment: def
Initial amount: 0.0
 
 s26
Compartment: def
Initial amount: 0.0
 
 s27
Compartment: def
Initial amount: 0.0
 
 s28
Compartment: def
Initial amount: 0.0
 
 s29
Compartment: def
Initial amount: 0.0
 
 s30
Compartment: def
Initial amount: 0.0
 
 s31
Compartment: def
Initial amount: 0.0
 
 s32
Compartment: def
Initial amount: 0.0
 
 s33
Compartment: def
Initial amount: 0.0
 
 s34
Compartment: def
Initial amount: 0.0
 
 s35
Compartment: def
Initial amount: 0.0
 
 s36
Compartment: def
Initial amount: 0.0
 
 s37
Compartment: def
Initial amount: 0.0
 
 s38
Compartment: def
Initial amount: 0.0
 
 s39
Compartment: def
Initial amount: 0.0
 
 s40
Compartment: def
Initial amount: 0.0
 
 s41
Compartment: def
Initial amount: 0.0
 
 s42
Compartment: def
Initial amount: 0.0
 
 s43
Compartment: def
Initial amount: 0.0
 
 s44
Compartment: def
Initial amount: 0.0
 
 s45
Compartment: def
Initial amount: 0.0
 
 s46
Compartment: def
Initial amount: 0.0
 
 s47
Compartment: def
Initial amount: 0.0
 
 s48
Compartment: def
Initial amount: 0.0
 
 s49
Compartment: def
Initial amount: 0.0
 
 s50
Compartment: def
Initial amount: 0.0
 
 s51
Compartment: def
Initial amount: 0.0
 
Global Parameters (120)
 
   n1
Value: 2.6
Constant
 
   n2
Value: 0.64
Constant
 
   n3
Value: 0.29
Constant
 
   n4
Value: 0.07
Constant
 
   n5
Value: 0.23
Constant
 
   n6
Value: 20.0
Constant
 
   n7
Value: 0.2
Constant
 
   n8
Value: 0.5
Constant
 
   n9
Value: 0.2
Constant
 
   n10
Value: 0.4
Constant
 
   n11
Value: 0.6
Constant
 
   n12
Value: 12.5
Constant
 
   n13
Value: 1.3
Constant
 
   n14
Value: 0.1
Constant
 
   g1
Value: 0.1
Constant
 
   g2
Value: 0.01
Constant
 
   g3
Value: 0.6
Constant
 
   g4
Value: 0.01
Constant
 
   g5
Value: 0.15
Constant
 
   g6
Value: 0.3
Constant
 
   g7
Value: 0.6
Constant
 
   g8
Value: 0.01
Constant
 
   g9
Value: 0.3
Constant
 
 g10
Value: 0.5
Constant
 
   g11
Value: 0.7
Constant
 
   g12
Value: 0.2
Constant
 
   g13
Value: 1.0
Constant
 
   g14
Value: 0.0040
Constant
 
   g15
Value: 0.4
Constant
 
   g16
Value: 0.3
Constant
 
   m1
Value: 0.54
Constant
 
   m2
Value: 0.24
Constant
 
   m3
Value: 0.2
Constant
 
   m4
Value: 0.2
Constant
 
   m5
Value: 0.3
Constant
 
   m6
Value: 0.3
Constant
 
   m7
Value: 0.7
Constant
 
   m8
Value: 0.4
Constant
 
   m9
Value: 1.1
Constant
 
   m10
Value: 1.0
Constant
 
   m11
Value: 1.0
Constant
 
   m12
Value: 1.0
Constant
 
   m13
Value: 0.32
Constant
 
   m14
Value: 0.4
Constant
 
   m15
Value: 0.7
Constant
 
   m16
Value: 0.5
Constant
 
   m17
Value: 0.5
Constant
 
   m18
Value: 3.4
Constant
 
   m19
Value: 0.2
Constant
 
   m20
Value: 0.6
Constant
 
   m21
Value: 0.08
Constant
 
   m22
Value: 0.1
Constant
 
 m23
Value: 1.8
Constant
 
   m24
Value: 0.1
Constant
 
   m25
Value: 1.8
Constant
 
   m26
Value: 0.5
Constant
 
   m27
Value: 0.1
Constant
 
   m28
Value: 20.0
Constant
 
   m29
Value: 5.0
Constant
 
   m30
Value: 3.0
Constant
 
   m31
Value: 0.3
Constant
 
   m32
Value: 0.2
Constant
 
   m33
Value: 13.0
Constant
 
   m34
Value: 0.6
Constant
 
   m35
Value: 0.3
Constant
 
   m36
Value: 0.1
Constant
 
   m37
Value: 0.8
Constant
 
   m38
Value: 0.5
Constant
 
   m39
Value: 0.3
Constant
 
   a
Value: 2.0
Constant
 
   b
Value: 2.0
Constant
 
   c
Value: 2.0
Constant
 
 d
Value: 2.0
Constant
 
   e
Value: 2.0
Constant
 
   f
Value: 2.0
Constant
 
   p1
Value: 0.13
Constant
 
   p2
Value: 0.27
Constant
 
   p3
Value: 0.1
Constant
 
   p4
Value: 0.56
Constant
 
   p5
Value: 4.0
Constant
 
   p6
Value: 0.6
Constant
 
   p7
Value: 0.3
Constant
 
   p8
Value: 0.6
Constant
 
   p9
Value: 0.8
Constant
 
   p10
Value: 0.54
Constant
 
   p11
Value: 0.51
Constant
 
   p12
Value: 3.4
Constant
 
   p13
Value: 0.1
Constant
 
   p14
Value: 0.14
Constant
 
   p15
Value: 3.0
Constant
 
   p16
Value: 0.62
Constant
 
   p17
Value: 4.8
Constant
 
   p18
Value: 4.0
Constant
 
   p19
Value: 1.0
Constant
 
   p20
Value: 0.1
Constant
 
   p21
Value: 1.0
Constant
 
   p22
Value: 0.5
Constant
 
   p23
Value: 0.37
Constant
 
   p24
Value: 10.0
Constant
 
   p25
Value: 8.0
Constant
 
   p26
Value: 0.3
Constant
 
   p27
Value: 0.8
Constant
 
   p28
Value: 2.0
Constant
 
   p29
Value: 0.1
Constant
 
   p30
Value: 0.9
Constant
 
   p31
Value: 0.1
Constant
 
   q1
Value: 1.2
Constant
 
   q2
Value: 1.56
Constant
 
   q3
Value: 2.8
Constant
 
 L
Value: 1.0   (Units: time)
Constant
 
 D
Constant
 
   E34
Value: 1.0
Constant
 
 Gn
Value: 1.0
Constant
 
 EGn
Value: 1.0
Constant
 
 lightOffset
Constant
 
 cyclePeriod
Value: 24.0   (Units: time)
Constant
 
   lightAmplitude
Value: 1.0   (Units: time)
Constant
 
   phase
Constant
 
   twilightPeriod
Value: 0.05   (Units: time)
Constant
 
   photoPeriod
Value: 12.0   (Units: time)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000412

Curator's comment: (updated: 04 Apr 2012 13:29:08 BST)

The plots corresponding to WT (Wild Type) in figure 2C of the reference publication has been reproduced here. The data were obtained by simulating the model using Copasi v4.8 (Build 35) and plotted using Gnuplot.

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