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BIOMD0000000445 - Pokhilko2013 - TOC1 signalling in Arabidopsis circadian clock

 

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Reference Publication
Publication ID: 23506153
Pokhilko A, Mas P, Millar AJ.
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs.
BMC Syst Biol 2013; 7: 23
School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JH, UK.  [more]
Model
Original Model: Pokhilko_2012_Arabidopsis_...
Submitter: Alexandra Pokhilko
Submission ID: MODEL1209110002
Submission Date: 11 Sep 2012 20:28:16 UTC
Last Modification Date: 16 Apr 2014 13:24:56 UTC
Creation Date: 22 Mar 2013 12:36:55 UTC
Encoders:  Vijayalakshmi Chelliah
   Alexandra Pokhilko
set #1
bqbiol:isVersionOf Gene Ontology circadian rhythm
set #2
bqbiol:hasTaxon Taxonomy Arabidopsis thaliana
set #3
bqmodel:isDerivedFrom BioModels Database Pokhilko2012_CircClock_RepressilatorFeedbackloop
Notes
Pokhilko2013 - TOC1 signalling in Arabidopsis circadian clock

In this model, Pokhilko et al. has incorporated the negative transcriptional regulations of the core clock genes by TOC1 and the up-regulation of TOC1 expression by ABA signalling, to their previous model BIOMD0000000412

This model is described in the article:

Pokhilko A, Mas P, Millar AJ.
BMC Syst Biol 2013; 7: 23

Abstract:

BACKGROUND: 24-hour biological clocks are intimately connected to the cellular signalling network, which complicates the analysis of clock mechanisms. The transcriptional regulator TOC1 (TIMING OF CAB EXPRESSION 1) is a founding component of the gene circuit in the plant circadian clock. Recent results show that TOC1 suppresses transcription of multiple target genes within the clock circuit, far beyond its previously-described regulation of the morning transcription factors LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN CLOCK ASSOCIATED 1). It is unclear how this pervasive effect of TOC1 affects the dynamics of the clock and its outputs. TOC1 also appears to function in a nested feedback loop that includes signalling by the plant hormone Abscisic Acid (ABA), which is upregulated by abiotic stresses, such as drought. ABA treatments both alter TOC1 levels and affect the clock's timing behaviour. Conversely, the clock rhythmically modulates physiological processes induced by ABA, such as the closing of stomata in the leaf epidermis. In order to understand the dynamics of the clock and its outputs under changing environmental conditions, the reciprocal interactions between the clock and other signalling pathways must be integrated. RESULTS: We extended the mathematical model of the plant clock gene circuit by incorporating the repression of multiple clock genes by TOC1, observed experimentally. The revised model more accurately matches the data on the clock's molecular profiles and timing behaviour, explaining the clock's responses in TOC1 over-expression and toc1 mutant plants. A simplified representation of ABA signalling allowed us to investigate the interactions of ABA and circadian pathways. Increased ABA levels lengthen the free-running period of the clock, consistent with the experimental data. Adding stomatal closure to the model, as a key ABA- and clock-regulated downstream process allowed to describe TOC1 effects on the rhythmic gating of stomatal closure. CONCLUSIONS: The integrated model of the circadian clock circuit and ABA-regulated environmental sensing allowed us to explain multiple experimental observations on the timing and stomatal responses to genetic and environmental perturbations. These results crystallise a new role of TOC1 as an environmental sensor, which both affects the pace of the central oscillator and modulates the kinetics of downstream processes.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 23506153 Submission Date: 11 Sep 2012 20:28:16 UTC Last Modification Date: 16 Apr 2014 13:24:56 UTC Creation Date: 22 Mar 2013 12:36:55 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
cABAR_m_trscr cABAR_m_degr cPP2C_act cPP2C_degr
cSnRK2_degr cSnRK2_act cs_act cs_degr
Rules
Assignment Rule (variable: L) Assignment Rule (variable: D)    
Physical entities
Compartments Species
default cABAR_m cPP2C cSnRK2
cs    
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    
No Name      
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 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 q1
q2 q3 L D
lightOffset cyclePeriod lightAmplitude phase
twilightPeriod photoPeriod g17 g18
g19 g20 g21 g22
g n15 h i
j g23 g24 g25
g26 g27 g28 g29
m38 m39 n18 n16
quantity n17 n19 p31
p32 p33 A0  
Reactions (64)
 
 cL_m_trscr  → [cL_m];   {cP} , {cP9} , {cP7} , {cNI} , {cT} , {cNI} , {cP} , {cP7} , {cP9} , {cT}
 
 cL_m_degr [cL_m] → ;   {cL_m}
 
 cL_trsl  → [cL];   {cL_m} , {cL_m}
 
 cL_degr [cL] → ;   {cL}
 
 cL_modif  → [cLm];   {cL} , {cL}
 
 cLm_degr [cLm] → ;   {cLm}
 
 cP_trsl  → [cP];   {cP}
 
 cP_degr [cP] → ;   {cP}
 
 cP9_m_trscr  → [cP9_m];   {cP} , {cL} , {cEC} , {cT} , {cEC} , {cL} , {cP} , {cT}
 
 cP9_m_degr [cP9_m] → ;   {cP9_m}
 
 cP9_trsl  → [cP9];   {cP9_m} , {cP9_m}
 
 cP9_degr [cP9] → ;   {cP9}
 
 cP7_m_trscr  → [cP7_m];   {cLm} , {cL} , {cP9} , {cT} , {cL} , {cLm} , {cP9} , {cT}
 
 cP7_m_degr [cP7_m] → ;   {cP7_m}
 
 cP7_trsl  → [cP7];   {cP7_m} , {cP7_m}
 
 cP7_degr [cP7] → ;   {cP7}
 
 cNI_m_trscr  → [cNI_m];   {cT} , {cLm} , {cP7} , {cLm} , {cP7} , {cT}
 
 cNI_m_degr [cNI_m] → ;   {cNI_m}
 
 cNI_trsl  → [cNI];   {cNI_m} , {cNI_m}
 
 cNI_degr [cNI] → ;   {cNI}
 
 cT_m_trscr  → [cT_m];   {cL} , {cSnRK2} , {cEC} , {cEC} , {cL} , {cSnRK2}
 
 cT_m_degr [cT_m] → ;   {cT_m}
 
 cT_trsl  → [cT];   {cT_m} , {cT_m}
 
 cT_degr [cT] → ;   {cZTL} , {cZG} , {cT} , {cZG} , {cZTL}
 
 cE4_m_trscr  → [cE4_m];   {cT} , {cEC} , {cL} , {cEC} , {cL} , {cT}
 
 cE4_m_degr [cE4_m] → ;   {cE4_m}
 
 cE4_trsl  → [cE4];   {cE4_m} , {cE4_m}
 
 cE4_degr [cE4] → ;   {cE3n} , {cLUX} , {cCOP1d} , {cCOP1n} , {cCOP1d} , {cCOP1n} , {cE3n} , {cE4} , {cLUX}
 
 cE3_m_trscr  → [cE3_m];   {cL} , {cL}
 
 cE3_m_degr [cE3_m] → ;   {cE3_m}
 
 cE3_trsl  → [cE3];   {cE3_m} , {cE3_m}
 
 cE3_degr [cE3] → ;   {cCOP1c} , {cCOP1c} , {cE3}
 
 cE3n_import [cE3] → [cE3n];   {cE3} , {cE3n}
 
 cE3n_degr [cE3n] → ;   {cCOP1n} , {cCOP1d} , {cE4} , {cLUX} , {cG} , {cE3n} , {cCOP1d} , {cCOP1n} , {cE3n} , {cE4} , {cG} , {cLUX}
 
 cLUX_m_trscr  → [cLUX_m];   {cT} , {cEC} , {cL} , {cEC} , {cL} , {cT}
 
 cLUX_m_degr [cLUX_m] → ;   {cLUX_m}
 
 cLUX_trsl  → [cLUX];   {cLUX_m} , {cLUX_m}
 
 cLUX_degr [cLUX] → ;   {cE4} , {cE3n} , {cCOP1d} , {cCOP1n} , {cCOP1d} , {cCOP1n} , {cE3n} , {cE4} , {cLUX}
 
 cCOP1c_trsl  → [cCOP1c];  
 
 cCOP1c_degr [cCOP1c] → ;   {cCOP1c}
 
 cCOP1n_import [cCOP1c] → [cCOP1n];   {cCOP1c}
 
 cCOP1n_degr [cCOP1n] → ;   {cCOP1n}
 
 cCOP1d_activ [cCOP1n] → [cCOP1d];   {cP} , {cCOP1n} , {cP}
 
 cCOP1d_degr [cCOP1d] → ;   {cCOP1d}
 
 cG_m_trscr  → [cG_m];   {cT} , {cP} , {cEC} , {cL} , {cEC} , {cL} , {cP} , {cT}
 
 cG_m_degr [cG_m] → ;   {cG_m}
 
 cG_trsl  → [cG];   {cG_m} , {cG_m}
 
 cG_degr [cG] → ;   {cE3n} , {cE3n} , {cG}
 
 cG_cZTL_assoc [cG] + [cZTL] ↔ [cZG];   {cG} , {cZG} , {cZTL}
 
 cZTL_trsl  → [cZTL];  
 
 cZTL_degr [cZTL] → ;   {cZTL}
 
 cZG_degr [cZG] → ;   {cZG}
 
 cG_cE3_assoc [cE3] + [cG] → [cEG];   {cE3} , {cG}
 
 cEG_degr [cEG] → ;   {cCOP1c} , {cE3n} , {cG} , {cCOP1n} , {cCOP1d} , {cCOP1c} , {cCOP1d} , {cCOP1n} , {cE3n} , {cEG} , {cG}
 
 cEC_form  → [cEC];   {cLUX} , {cE4} , {cE3n} , {cCOP1d} , {cCOP1n} , {cCOP1d} , {cCOP1n} , {cE3n} , {cE4} , {cLUX}
 
 cEC_degr [cEC] → ;   {cCOP1n} , {cCOP1d} , {cG} , {cE3n} , {cEG} , {cCOP1d} , {cCOP1n} , {cE3n} , {cEC} , {cEG} , {cG}
 
 cABAR_m_trscr  → [cABAR_m];   {cT} , {cL} , {cL} , {cT}
 
 cABAR_m_degr [cABAR_m] → ;   {cABAR_m}
 
 cPP2C_act  → [cPP2C];   {cABAR_m} , {cABAR_m}
 
 cPP2C_degr [cPP2C] → ;   {cPP2C}
 
 cSnRK2_degr [cSnRK2] → ;   {cPP2C} , {cPP2C} , {cSnRK2}
 
 cSnRK2_act  → [cSnRK2];  
 
 cs_act  → [cs];   {cs} , {cSnRK2} , {cSnRK2} , {cs}
 
 cs_degr [cs] → ;   {cs}
 
Rules (2)
 
 Assignment Rule (name: L) L = lightOffset+0.5*lightAmplitude*(1+tanh(cyclePeriod*((time+phase)/cyclePeriod-floor(floor(time+phase)/cyclePeriod))/twilightPeriod))-0.5*lightAmplitude*(1+tanh((cyclePeriod*((time+phase)/cyclePeriod-floor(floor(time+phase)/cyclePeriod))-photoPeriod)/twilightPeriod))+0.5*lightAmplitude*(1+tanh((cyclePeriod*((time+phase)/cyclePeriod-floor(floor(time+phase)/cyclePeriod))-cyclePeriod)/twilightPeriod))
 
 Assignment Rule (name: D) D = 1-L
 
Functions (64)
 
 function_4_cE4_degr lambda(cCOP1d, cCOP1n, cE3n, cE4, cLUX, def, m10, m35, m9, p21, p25, p26, (m35*cE4+p25*cE4*cE3n-p21*p25*cE4*cE3n/(p26*cLUX+p21+m9*cCOP1d+m10*cCOP1n))/def)
 
 function_4_cE3_m_trscr lambda(cL, def, e, g16, n3, n3*g16^e/(cL^e+g16^e)/def)
 
 function_4_cE3_m_degr lambda(cE3_m, def, m26, m26*cE3_m/def)
 
 function_4_cE3_trsl lambda(cE3_m, def, p16, p16*cE3_m/def)
 
 function_4_cE3_degr lambda(cCOP1c, cE3, def, m9, m9*cE3*cCOP1c/def)
 
 function_4_cE3n_degr lambda(cCOP1d, cCOP1n, cE3n, cE4, cG, cLUX, def, m10, m19, m9, p17, p21, p25, p26, p28, p29, (m10*cE3n*cCOP1n+m9*cE3n*cCOP1d+p25*cE4*cE3n-p21*p25*cE4*cE3n/(p26*cLUX+p21+m9*cCOP1d+m10*cCOP1n)+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/def)
 
 function_4_cE3n_import lambda(cE3, cE3n, def, p19, p20, (p19*cE3-p20*cE3n)/def)
 
 function_4_cLUX_m_trscr lambda(cEC, cL, cT, def, e, g2, g6, n13, parameter_3, parameter_7, parameter_3^parameter_7/(parameter_3^parameter_7+cT^parameter_7)*n13*g2/(cEC+g2)*g6^e/(cL^e+g6^e)/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_1 lambda(cCOP1d, cCOP1n, cE3n, cE4, cLUX, def, m10, m36, m9, p21, p25, p26, (m36*cLUX+p26*cLUX*p25*cE4*cE3n/(p26*cLUX+p21+m9*cCOP1d+m10*cCOP1n))/def)
 
 function_4_cCOP1c_trsl lambda(def, n5, n5/def)
 
 function_4_cCOP1c_degr lambda(L, cCOP1c, m27, p15, m27*cCOP1c*(1+p15*L))
 
 function_4_cCOP1n_import lambda(cCOP1c, def, p6, p6*cCOP1c/def)
 
 function_4_cL_m_trscr lambda(L, a, cNI, cP, cP7, cP9, cT, g1, n1, q1, L*q1*cP+n1*g1^a/((cP9+cP7+cNI+cT)^a+g1^a))
 
 function_4_cL_m_degr lambda(L, cL_m, m1, m2, (m2+(m1-m2)*L)*cL_m)
 
 function_4_cL_trsl lambda(L, cL_m, p1, p2, cL_m*(p1*L+p2))
 
 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, p7, p7*(1-L)*(1-cP))
 
 function_4_cP_degr lambda(L, cP, m11, m11*cP*L)
 
 function_4_cP9_m_trscr_1 lambda(L, cEC, cL, cP, cT, e, g8, g9, n4, n7, parameter_2, parameter_7, q3, parameter_2^parameter_7/(parameter_2^parameter_7+cT^parameter_7)*(L*q3*cP+(n4+n7*cL^e/(cL^e+g9^e))*g8/(cEC+g8)))
 
 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(L, cP9, m13, m22, (m13+m22*(1-L))*cP9)
 
 function_4_cP7_m_trscr_1 lambda(cL, cLm, cP9, cT, def, e, f, g10, g11, n8, n9, parameter_6, parameter_7, parameter_6^parameter_7/(parameter_6^parameter_7+cT^parameter_7)*(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(L, cP7, m15, m23, (m15+m23*(1-L))*cP7)
 
 function_4_cNI_m_trscr_1 lambda(b, cLm, cP7, cT, def, e, g12, g13, n10, n11, parameter_12, parameter_7, parameter_12^parameter_7/(parameter_12^parameter_7+cT^parameter_7)*(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(L, cNI, m17, m24, (m17+m24*(1-L))*cNI)
 
 function_4_cT_m_trscr lambda(cEC, cL, def, e, g4, g5, n2, parameter_11, parameter_14, species_3, n2/(1+(cL/(g5*(1+(species_3/parameter_14)^parameter_11)))^e)*g4/(cEC+g4)/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(L, cT, cZG, cZTL, m6, m7, m8, p5, (m6+m7*(1-L))*cT*(p5*cZTL+cZG)+m8*cT)
 
 function_4_cE4_m_trscr_1 lambda(cEC, cL, cT, def, e, g6, parameter_4, parameter_5, parameter_7, parameter_8, parameter_5^parameter_7/(parameter_5^parameter_7+cT^parameter_7)*parameter_8*parameter_4/(cEC+parameter_4)*g6^e/(cL^e+g6^e)/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_cs_act_1 lambda(L, def, parameter_10, parameter_15, parameter_21, parameter_25, species_3, species_4, (parameter_25+parameter_21*L)*(1-species_4)*parameter_15^parameter_10/(parameter_15^parameter_10+species_3^parameter_10)/def)
 
 function_4_cs_degr_1 lambda(def, m29, species_4, m29*species_4/def)
 
 function_4_cCOP1n_degr lambda(L, cCOP1n, m27, p15, m27*cCOP1n*(1+p15*L))
 
 function_4_cCOP1d_degr lambda(L, cCOP1d, m31, m33, m31*(1+m33*(1-L))*cCOP1d)
 
 function_4_cCOP1d_activ lambda(L, cCOP1n, cP, n14, n6, n6*L*cP*cCOP1n+n14*cCOP1n)
 
 function_4_cG_m_trscr_1 lambda(L, cEC, cL, cP, cT, e, g14, g15, n12, parameter_1, parameter_7, q2, parameter_1^parameter_7/(parameter_1^parameter_7+cT^parameter_7)*(L*q2*cP+n12*g14/(cEC+g14)*g15^e/(cL^e+g15^e)))
 
 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_1 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(L, cG, cZG, cZTL, p12, p13, p12*L*cZTL*cG-p13*(1-L)*cZG)
 
 function_4_cZTL_trsl lambda(def, p14, p14/def)
 
 function_4_cZTL_degr lambda(cZTL, def, m20, m20*cZTL/def)
 
 function_4_cZG_degr lambda(cZG, def, m21, m21*cZG/def)
 
 function_4_cG_cE3_assoc lambda(cE3, cG, def, p17, p17*cE3*cG/def)
 
 function_4_cEG_degr_1 lambda(cCOP1c, cCOP1d, cCOP1n, cE3n, cEG, cG, def, m10, m19, m9, p17, p18, p28, p29, parameter_26, (m10*cEG*cCOP1c+p18*cEG-parameter_26*(p18*cEG+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/(m10*cCOP1n+m9*cCOP1d+parameter_26))/def)
 
 function_4_cEC_form lambda(cCOP1d, cCOP1n, cE3n, cE4, cLUX, def, m10, m9, p21, p25, p26, p26*cLUX*p25*cE4*cE3n/(p26*cLUX+p21+m9*cCOP1d+m10*cCOP1n)/def)
 
 function_4_cEC_degr lambda(L, cCOP1d, cCOP1n, cE3n, cEC, cEG, cG, d, g7, m10, m19, m32, m9, p17, p18, p24, p28, p29, parameter_26, m10*cCOP1n*cEC+m9*cCOP1d*cEC+m32*cEC*(1+p24*L*(p28*cG/(p29+m19+p17*cE3n)+(p18*cEG+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/(m10*cCOP1n+m9*cCOP1d+parameter_26))^d/((p28*cG/(p29+m19+p17*cE3n)+(p18*cEG+p17*cE3n*p28*cG/(p29+m19+p17*cE3n))/(m10*cCOP1n+m9*cCOP1d+parameter_26))^d+g7^d)))
 
 function_4_cABAR_m_trscr_1 lambda(cL, cT, def, e, parameter_13, parameter_17, parameter_24, parameter_7, parameter_13^parameter_7/(parameter_13^parameter_7+cT^parameter_7)*parameter_24*cL^e/(cL^e+parameter_17^e)/def)
 
 function_4_cABAR_m_degr lambda(def, m37, species_1, m37*species_1/def)
 
 function_4_cPP2C_act_1 lambda(def, parameter_16, parameter_18, parameter_28, parameter_29, parameter_9, species_1, parameter_28*parameter_16^parameter_9/((0.5*(parameter_29+species_1+parameter_18-((parameter_29+species_1+parameter_18)^2-4*parameter_29*species_1)^(1/2)))^parameter_9+parameter_16^parameter_9)/def)
 
 function_4_cPP2C_degr_1 lambda(def, parameter_20, species_2, parameter_20*species_2/def)
 
 function_4_cSnRK2_degr lambda(def, m30, species_2, species_3, m30*species_3*species_2/def)
 
 function_4_cSnRK2_act_1 lambda(def, parameter_27, parameter_27/def)
 
 default Spatial dimensions: 3.0  Compartment size: 1.0
 
 cABAR_m
Compartment: default
Initial concentration: 0.999999951844376
 
 cPP2C
Compartment: default
Initial concentration: 0.999999951844376
 
 cSnRK2
Compartment: default
Initial concentration: 0.999999951844376
 
   cs
Compartment: default
Initial concentration: 0.999999951844376
 
 def Spatial dimensions: 3.0  Compartment size: 1.0
 
 cCOP1c
Compartment: def
Initial concentration: 0.326899984257926
 
 cCOP1d
Compartment: def
Initial concentration: 0.256599987643267
 
 cCOP1n
Compartment: def
Initial concentration: 0.649999968698844
 
 cE3
Compartment: def
Initial concentration: 0.15029999276221
 
 cE3_m
Compartment: def
Initial concentration: 0.299099985596653
 
 cE3n
Compartment: def
Initial concentration: 0.0285999986227492
 
 cE4
Compartment: def
Initial concentration: 0.206999990031786
 
 cE4_m
Compartment: def
Initial concentration: 0.101199995126651
 
 cEC
Compartment: def
Initial concentration: 0.0708999965857662
 
 cEG
Compartment: def
Initial concentration: 0.00409999980256194
 
 cG
Compartment: def
Initial concentration: 0.0195999990561498
 
 cG_m
Compartment: def
Initial concentration: 0.101699995102573
 
 cL
Compartment: def
Initial concentration: 0.505999975633254
 
 cLUX
Compartment: def
Initial concentration: 0.575999972262361
 
 cLUX_m
Compartment: def
Initial concentration: 0.101199995126651
 
 cL_m
Compartment: def
Initial concentration: 1.01509995111723
 
 cLm
Compartment: def
Initial concentration: 0.0787999962053368
 
 cNI
Compartment: def
Initial concentration: 0.069699996643553
 
 cNI_m
Compartment: def
Initial concentration: 0.0730999964798238
 
 cP
Compartment: def
Initial concentration: 0.955999953963223
 
 cP7
Compartment: def
Initial concentration: 0.116699994380239
 
 cP7_m
Compartment: def
Initial concentration: 0.401599980660701
 
 cP9
Compartment: def
Initial concentration: 0.0237999988538961
 
 cP9_m
Compartment: def
Initial concentration: 0.0657999968313599
 
 cT
Compartment: def
Initial concentration: 0.0434999979052303
 
 cT_m
Compartment: def
Initial concentration: 0.0976999952951955
 
 cZG
Compartment: def
Initial concentration: 0.0754999963642504
 
 cZTL
Compartment: def
Initial concentration: 0.250499987937016
 
   No Name Spatial dimensions: 3.0  Compartment size: 1.0
Global Parameters (143)
 
 n1
Value: 2.6
Constant
 
 n2
Value: 0.35
Constant
 
 n3
Value: 0.29
Constant
 
 n4
Value: 0.04
Constant
 
 n5
Value: 0.4
Constant
 
 n6
Value: 20.0
Constant
 
 n7
Value: 0.1
Constant
 
 n8
Value: 0.5
Constant
 
 n9
Value: 0.6
Constant
 
 n10
Value: 0.3
Constant
 
 n11
Value: 0.6
Constant
 
 n12
Value: 9.0
Constant
 
 n13
Value: 2.0
Constant
 
 n14
Value: 0.1
Constant
 
 g1
Value: 0.1
Constant
 
 g2
Value: 0.01
Constant
 
 g3
Value: 0.6
Constant
 
 g4
Value: 0.0060
Constant
 
 g5
Value: 0.2
Constant
 
 g6
Value: 0.3
Constant
 
 g7
Value: 1.0
Constant
 
 g8
Value: 0.04
Constant
 
 g9
Value: 0.3
Constant
 
 g10
Value: 0.5
Constant
 
 g11
Value: 0.7
Constant
 
 g12
Value: 0.1
Constant
 
 g13
Value: 1.0
Constant
 
 g14
Value: 0.02
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: 0.2
Constant
 
 m7
Value: 0.1
Constant
 
 m8
Value: 0.5
Constant
 
 m9
Value: 0.2
Constant
 
 m10
Value: 0.1
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: 0.9
Constant
 
 m20
Value: 0.6
Constant
 
 m21
Value: 0.08
Constant
 
 m22
Value: 0.1
Constant
 
 m23
Value: 0.5
Constant
 
 m24
Value: 0.5
Constant
 
 m25
Value: 0.9
Constant
 
 m26
Value: 0.5
Constant
 
 m27
Value: 0.1
Constant
 
 m28
Value: 28.0
Constant
 
 m29
Value: 0.3
Constant
 
 m30
Value: 1.0
Constant
 
 m31
Value: 0.1
Constant
 
 m32
Value: 0.2
Constant
 
 m33
Value: 13.0
Constant
 
 m34
Value: 0.6
Constant
 
 m35
Value: 0.3
Constant
 
 m36
Value: 0.3
Constant
 
 m37
Value: 0.4
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: 0.5
Constant
 
 p5
Value: 1.0
Constant
 
 p6
Value: 0.2
Constant
 
 p7
Value: 0.3
Constant
 
 p8
Value: 0.6
Constant
 
 p9
Value: 0.8
Constant
 
 p10
Value: 0.54
Constant
 
 p11
Value: 0.5
Constant
 
 p12
Value: 10.0
Constant
 
 p13
Value: 0.1
Constant
 
 p14
Value: 0.14
Constant
 
 p15
Value: 2.0
Constant
 
 p16
Value: 0.62
Constant
 
 p17
Value: 17.0
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: 11.0
Constant
 
 p25
Value: 2.0
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
 
 q1
Value: 1.0
Constant
 
 q2
Value: 1.56
Constant
 
 q3
Value: 3.0
Constant
 
  L
Value: 0.5
 
  D
Value: 0.5
 
 lightOffset
Constant
 
 cyclePeriod
Value: 24.0
Constant
 
 lightAmplitude
Value: 1.0
Constant
 
 phase
Constant
 
   twilightPeriod
Value: 0.05
Constant
 
 photoPeriod
Value: 12.0
Constant
 
 g17
Value: 0.6
Constant
 
 g18
Value: 0.4
Constant
 
 g19
Value: 0.4
Constant
 
 g20
Value: 0.03
Constant
 
 g21
Value: 0.4
Constant
 
 g22
Value: 0.1
Constant
 
 g
Value: 2.0
Constant
 
 n15
Value: 2.0
Constant
 
 h
Value: 2.0
Constant
 
 i
Value: 2.0
Constant
 
 j
Value: 2.0
Constant
 
 g23
Value: 0.6
Constant
 
 g24
Value: 0.3
Constant
 
 g25
Value: 0.5
Constant
 
 g26
Value: 0.3
Constant
 
 g27
Value: 0.2
Constant
 
 g28
Value: 0.1
Constant
 
 g29
Value: 1.0
Constant
 
 m38
Value: 0.3
Constant
 
 m39
Value: 0.2
Constant
 
 n18
Value: 0.5
Constant
 
 n16
Constant
 
   quantity
Constant
 
 n17
Value: 0.5
Constant
 
 n19
Value: 0.2
Constant
 
 p31
Value: 0.1
Constant
 
 p32
Value: 0.1
Constant
 
 p33
Value: 0.2
Constant
 
   A0
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000445

Curator's comment: (updated: 22 Mar 2013 12:34:55 GMT)

The model reproduces figure 3a of the reference publication. The plot data were obtained by simulating the model in Copasi v4.3 (Build 35). The plot was generated using Gnuplot.

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