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BIOMD0000000097 - Zeilinger2006_PRR7-PRR9light-Yprime

 

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Reference Publication
Publication ID: 17102803
Zeilinger MN, Farré EM, Taylor SR, Kay SA, Doyle FJ 3rd.
A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9.
Mol. Syst. Biol. 2006; 2: 58
Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA.  [more]
Model
Original Model: BIOMD0000000097.xml.origin
Submitter: Molecular Systems Biology
Submission ID: MODEL4025650992
Submission Date: 13 Mar 2007 22:26:59 UTC
Last Modification Date: 05 Jul 2012 14:41:50 UTC
Creation Date: 11 Dec 2006 17:12:17 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:is KEGG Pathway ath04710
Gene Ontology circadian rhythm
bqmodel:isDerivedFrom BioModels Database Locke2005_CircadianClock
set #2
bqbiol:occursIn Taxonomy Arabidopsis
Notes

The model reproduces the time profile of TOC1 and Y mRNA for a 8:16 cycle as depicted in Fig7A and 7B. A simple algorithm in the event section accomplishes the 8 hour light and 16 hour dark cycle. The model was successfully tested on MathSBML


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.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 17102803 Submission Date: 13 Mar 2007 22:26:59 UTC Last Modification Date: 05 Jul 2012 14:41:50 UTC Creation Date: 11 Dec 2006 17:12:17 UTC
Mathematical expressions
Reactions
Light dependent cLm production Light independent cLm production cLm degradation cLc synthesis
cLc transport to nucleus cLn transport to cytoplasm cLc degradation cLn degradation
cTm transcription cTm degradation cTc synthesis cTc transport to nucleus
cTn transport to cytoplasm cTc degradation cTn degradation Species X transcription
Species X degradation cXc synthesis cXc transport to nucleus cXn transport to cytoplasm
cXc degradation cXn degradation Species Y transcription cYm degradation
cYc synthesis cYc transport to nucleus cYn transport to cytoplasm cYc degradation
cYn degradation cPn synthesis cPn degradation cPn light dependent degradation
cP7m transcription cP7m degradation cP7c synthesis cP7c transport to nucleus
cP7n transport to cytoplasm cP7c degradation cP7n degradation cP9m transcription
cP9m degradation cP9c synthesis cP9c transport to nucleus cP9n transport to cytoplasm
cP9c degradation cP9n degradation    
Events
event_0000001 event_0000002    
Physical entities
Compartments Species
cytoplasm cLc cP7c cP9c
cTc cXc cYc
     
nucleus cLm cLn cP7m
cP7n cP9m cP9n
cPn cTm cTn
cXm cXn cYm
cYn    
Global parameters
q1 n1 g1 m1
k1 p1 r1 r2
m2 k2 m3 k3
n2 g2 g3 m4
k4 p2 p3 r5
r6 m10 k8 m11
k9 n4 n5 g5
g6 m12 k10 r3
r4 m5 m6 k5
m7 m8 k6 n3
g4 m9 k7 p4
r7 r8 m13 k11
m14 k12 p5 k13
q3 m15 g7 g8
n6 g9 m16 k14
p6 r9 r10 m17
k15 m18 k16 n7
g10 m19 k17 p7
r11 r12 m20 k18
m21 k19 q4 n8
a b c d
e f h i
j k ld lmax
Day_in_hours      
Reactions (46)
 
 Light dependent cLm production  → [cLm];   {cPn}
 
 Light independent cLm production  → [cLm];   {cXn} , {cP7n} , {cP9n}
 
 cLm degradation [cLm] → ;  
 
 cLc synthesis  → [cLc];   {cLm}
 
 cLc transport to nucleus [cLc] → [cLn];  
 
 cLn transport to cytoplasm [cLn] → [cLc];  
 
 cLc degradation [cLc] → ;  
 
 cLn degradation [cLn] → ;  
 
 cTm transcription  → [cTm];   {cYn} , {cLn}
 
 cTm degradation [cTm] → ;  
 
 cTc synthesis  → [cTc];   {cTm}
 
 cTc transport to nucleus [cTc] → [cTn];  
 
 cTn transport to cytoplasm [cTn] → [cTc];  
 
 cTc degradation [cTc] → ;  
 
 cTn degradation [cTn] → ;  
 
 Species X transcription  → [cXm];   {cTn}
 
 Species X degradation [cXm] → ;  
 
 cXc synthesis  → [cXc];   {cXm}
 
 cXc transport to nucleus [cXc] → [cXn];  
 
 cXn transport to cytoplasm [cXn] → [cXc];  
 
 cXc degradation [cXc] → ;  
 
 cXn degradation [cXn] → ;  
 
 Species Y transcription  → [cYm];   {cTn} , {cLn} , {cPn}
 
 cYm degradation [cYm] → ;  
 
 cYc synthesis  → [cYc];   {cYm}
 
 cYc transport to nucleus [cYc] → [cYn];  
 
 cYn transport to cytoplasm [cYn] → [cYc];  
 
 cYc degradation [cYc] → ;  
 
 cYn degradation [cYn] → ;  
 
 cPn synthesis  → [cPn];  
 
 cPn degradation [cPn] → ;  
 
 cPn light dependent degradation [cPn] → ;  
 
 cP7m transcription  → [cP7m];   {cLn}
 
 cP7m degradation [cP7m] → ;  
 
 cP7c synthesis  → [cP7c];   {cP7m}
 
 cP7c transport to nucleus [cP7c] → [cP7n];  
 
 cP7n transport to cytoplasm [cP7n] → [cP7c];  
 
 cP7c degradation [cP7c] → ;  
 
 cP7n degradation [cP7n] → ;  
 
 cP9m transcription  → [cP9m];   {cPn} , {cLn}
 
 cP9m degradation [cP9m] → ;  
 
 cP9c synthesis  → [cP9c];   {cP9m}
 
 cP9c transport to nucleus [cP9c] → [cP9n];  
 
 cP9n transport to cytoplasm [cP9n] → [cP9c];  
 
 cP9c degradation [cP9c] → ;  
 
 cP9n degradation [cP9n] → ;  
 
Events (2)
 
 event_0000001
Day_in_hours = Day_in_hours+24
ld = 1
 
 event_0000002
ld = 0
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 cLc
Compartment: cytoplasm
Initial concentration: 0.0659
 
 cP7c
Compartment: cytoplasm
Initial concentration: 0.0861
 
 cP9c
Compartment: cytoplasm
Initial concentration: 0.0077
 
 cTc
Compartment: cytoplasm
Initial concentration: 0.7852
 
   cXc
Compartment: cytoplasm
Initial concentration: 2.5615
 
   cYc
Compartment: cytoplasm
Initial concentration: 7.6795
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 cLm
Compartment: nucleus
Initial concentration: 0.1951
 
 cLn
Compartment: nucleus
Initial concentration: 0.3952
 
 cP7m
Compartment: nucleus
Initial concentration: 0.0772
 
 cP7n
Compartment: nucleus
Initial concentration: 2.7182
 
 cP9m
Compartment: nucleus
Initial concentration: 0.0011
 
 cP9n
Compartment: nucleus
Initial concentration: 0.0073
 
   cPn
Compartment: nucleus
Initial concentration: 0.0
 
 cTm
Compartment: nucleus
Initial concentration: 0.1234
 
 cTn
Compartment: nucleus
Initial concentration: 4.5209
 
 cXm
Compartment: nucleus
Initial concentration: 1.6104
 
 cXn
Compartment: nucleus
Initial concentration: 14.5474
 
 cYm
Compartment: nucleus
Initial concentration: 1.1149
 
 cYn
Compartment: nucleus
Initial concentration: 9.7016
 
Global Parameters (93)
 
   q1
Value: 13.4334   (Units: Hour_inv)
Constant
 
   n1
Value: 3.2016   (Units: nM_per_hour)
Constant
 
   g1
Value: 9.041   (Units: nM)
Constant
 
   m1
Value: 6.8248   (Units: nM_per_hour)
Constant
 
   k1
Value: 13.0594   (Units: nM)
Constant
 
   p1
Value: 0.6926   (Units: Hour_inv)
Constant
 
   r1
Value: 25.6818   (Units: Hour_inv)
Constant
 
   r2
Value: 3.9781   (Units: Hour_inv)
Constant
 
   m2
Value: 9.4099   (Units: nM_per_hour)
Constant
 
   k2
Value: 30.5639   (Units: nM)
Constant
 
   m3
Value: 13.7795   (Units: nM_per_hour)
Constant
 
   k3
Value: 33.514   (Units: nM)
Constant
 
   n2
Value: 11.6086   (Units: nM_per_hour)
Constant
 
   g2
Value: 16.6598   (Units: nM)
Constant
 
   g3
Value: 13.4112   (Units: nM)
Constant
 
   m4
Value: 12.1232   (Units: nM_per_hour)
Constant
 
   k4
Value: 1.3722   (Units: nM)
Constant
 
   p2
Value: 0.5403   (Units: Hour_inv)
Constant
 
   p3
Value: 6.9124   (Units: Hour_inv)
Constant
 
   r5
Value: 29.4607   (Units: Hour_inv)
Constant
 
   r6
Value: 4.5034   (Units: Hour_inv)
Constant
 
   m10
Value: 8.5523   (Units: nM_per_hour)
Constant
 
   k8
Value: 12.528   (Units: nM)
Constant
 
   m11
Value: 23.5996   (Units: nM_per_hour)
Constant
 
   k9
Value: 15.0626   (Units: nM)
Constant
 
   n4
Value: 1.7832   (Units: nM_per_hour)
Constant
 
   n5
Value: 7.4615   (Units: nM_per_hour)
Constant
 
   g5
Value: 1.5987   (Units: nM)
Constant
 
   g6
Value: 16.489   (Units: nM)
Constant
 
   m12
Value: 5.9504   (Units: nM_per_hour)
Constant
 
   k10
Value: 11.5688   (Units: nM)
Constant
 
   r3
Value: 51.1965   (Units: Hour_inv)
Constant
 
   r4
Value: 8.9147   (Units: Hour_inv)
Constant
 
   m5
Value: 7.2129   (Units: nM_per_hour)
Constant
 
   m6
Value: 9.5754   (Units: nM_per_hour)
Constant
 
   k5
Value: 34.2078   (Units: nM)
Constant
 
   m7
Value: 1.1032   (Units: nM_per_hour)
Constant
 
   m8
Value: 2.2006   (Units: nM_per_hour)
Constant
 
   k6
Value: 56.7596   (Units: nM)
Constant
 
   n3
Value: 2.4751   (Units: nM_per_hour)
Constant
 
   g4
Value: 20.5277   (Units: nM)
Constant
 
   m9
Value: 4.2193   (Units: nM_per_hour)
Constant
 
   k7
Value: 14.9114   (Units: nM)
Constant
 
   p4
Value: 6.0042   (Units: Hour_inv)
Constant
 
   r7
Value: 35.7842   (Units: Hour_inv)
Constant
 
   r8
Value: 27.9229   (Units: Hour_inv)
Constant
 
   m13
Value: 7.5959   (Units: nM_per_hour)
Constant
 
   k11
Value: 26.9638   (Units: nM)
Constant
 
   m14
Value: 8.1796   (Units: nM_per_hour)
Constant
 
   k12
Value: 21.8348   (Units: nM)
Constant
 
   p5
Value: 0.5   (Units: nM_per_hour)
Constant
 
   k13
Value: 1.2   (Units: nM)
Constant
 
   q3
Value: 1.0   (Units: Hour_inv)
Constant
 
   m15
Value: 1.2   (Units: nM_per_hour)
Constant
 
   g7
Value: 0.2778   (Units: nM)
Constant
 
   g8
Value: 0.9187   (Units: nM)
Constant
 
   n6
Value: 11.0924   (Units: nM_per_hour)
Constant
 
   g9
Value: 20.3795   (Units: nM)
Constant
 
   m16
Value: 9.3186   (Units: nM_per_hour)
Constant
 
   k14
Value: 51.261   (Units: nM)
Constant
 
   p6
Value: 9.8416   (Units: Hour_inv)
Constant
 
   r9
Value: 24.5689   (Units: Hour_inv)
Constant
 
   r10
Value: 0.5024   (Units: Hour_inv)
Constant
 
   m17
Value: 3.6143   (Units: nM_per_hour)
Constant
 
   k15
Value: 32.939   (Units: nM)
Constant
 
   m18
Value: 6.7455   (Units: nM_per_hour)
Constant
 
   k16
Value: 24.451   (Units: nM)
Constant
 
   n7
Value: 0.1031   (Units: nM_per_hour)
Constant
 
   g10
Value: 5.8418   (Units: nM)
Constant
 
   m19
Value: 1.9234   (Units: nM_per_hour)
Constant
 
   k17
Value: 9.8065   (Units: nM)
Constant
 
   p7
Value: 1.5323   (Units: Hour_inv)
Constant
 
   r11
Value: 25.7542   (Units: Hour_inv)
Constant
 
   r12
Value: 27.2451   (Units: Hour_inv)
Constant
 
   m20
Value: 3.7484   (Units: nM_per_hour)
Constant
 
   k18
Value: 25.9739   (Units: nM)
Constant
 
   m21
Value: 0.0193   (Units: nM_per_hour)
Constant
 
   k19
Value: 21.6441   (Units: nM)
Constant
 
   q4
Value: 6.274   (Units: Hour_inv)
Constant
 
   n8
Value: 3.5262   (Units: nM)
Constant
 
   a
Value: 1.2497   (Units: dimensionless)
Constant
 
   b
Value: 4.2126   (Units: dimensionless)
Constant
 
   c
Value: 1.4509   (Units: dimensionless)
Constant
 
   d
Value: 1.3058   (Units: dimensionless)
Constant
 
   e
Value: 2.4146   (Units: dimensionless)
Constant
 
   f
Value: 2.1349   (Units: dimensionless)
Constant
 
   h
Value: 1.4176   (Units: dimensionless)
Constant
 
   i
Value: 2.0074   (Units: dimensionless)
Constant
 
   j
Value: 1.7615   (Units: dimensionless)
Constant
 
   k
Value: 3.8877   (Units: dimensionless)
Constant
 
   ld
Value: 1.0   (Units: dimensionless)
 
   lmax
Value: 1.0   (Units: dimensionless)
Constant
 
   Day_in_hours
Value: 24.0   (Units: hour)
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000097

Curator's comment: (updated: 13 Mar 2007 01:21:45 GMT)

Shown above are time profiles of TOC1 mRNA and Y mRNA for a 8:16 light/dark cycle as depicted in Fig 7A and 7B of the paper. Simulation results obtained from MathSBML.

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