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BIOMD0000000185 - Locke2008_Circadian_Clock

 

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Reference Publication
Publication ID: 18312618
Locke JC, Westermark PO, Kramer A, Herzel H.
Global parameter search reveals design principles of the mammalian circadian clock.
BMC Syst Biol 2008; 2: 22
Institute for Theoretical Biology, Humboldt-University Berlin, 10115 Berlin, Germany. jlocke@caltech.edu.  [more]
Model
Original Model: BIOMD0000000185.origin
Submitter: Harish Dharuri
Submission ID: MODEL9223733527
Submission Date: 20 Aug 2008 19:45:09 UTC
Last Modification Date: 11 Jul 2012 17:47:04 UTC
Creation Date: 20 Aug 2008 08:10:29 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf Gene Ontology circadian regulation of gene expression
Gene Ontology circadian behavior
set #2
bqbiol:hasTaxon Taxonomy Mammalia
Notes

The model reproduces Fig 2A of the paper. Model successfully reproduced using Jarnac and 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: 18312618 Submission Date: 20 Aug 2008 19:45:09 UTC Last Modification Date: 11 Jul 2012 17:47:04 UTC Creation Date: 20 Aug 2008 08:10:29 UTC
Mathematical expressions
Reactions
Transcription mRNA degradation Neuropeptide dependent transcription activation Light dependent transcription activation
Translation Protein degradation Transcriptional repressor synthesis Transcriptional repressor degradation
Neuropeptide synthesis Neuropeptide degradation Transcription mRNA degradation
Neuropeptide dependent transcription activation Light dependent transcription activation Translation Protein degradation
Transcriptional repressor synthesis Transcriptional repressor degradation Neuropeptide synthesis Neuropeptide degradation
Rules
Assignment Rule (variable: F)      
Physical entities
Compartments Species
Cell clock gene mRNA clock protein Transcriptional repressor
Neuropeptide clock gene mRNA clock protein
Transcriptional repressor Neuropeptide  
Global parameters
F v_1 K1 n
v_2 K2 vc K
Kc L k3 v_4
K4 k5 v_6 K6
k7 v_8 K8  
Reactions (20)
 
 Transcription  → [clock gene mRNA];   {Transcriptional repressor}
 
 mRNA degradation [clock gene mRNA] → ;  
 
 Neuropeptide dependent transcription activation  → [clock gene mRNA];  
 
 Light dependent transcription activation  → [clock gene mRNA];  
 
 Translation  → [clock protein];   {clock gene mRNA}
 
 Protein degradation [clock protein] → ;  
 
 Transcriptional repressor synthesis  → [Transcriptional repressor];   {clock protein}
 
 Transcriptional repressor degradation [Transcriptional repressor] → ;  
 
 Neuropeptide synthesis  → [Neuropeptide];   {clock gene mRNA}
 
 Neuropeptide degradation [Neuropeptide] → ;  
 
 Transcription  → [clock gene mRNA];   {Transcriptional repressor}
 
 mRNA degradation [clock gene mRNA] → ;  
 
 Neuropeptide dependent transcription activation  → [clock gene mRNA];  
 
 Light dependent transcription activation  → [clock gene mRNA];  
 
 Translation  → [clock protein];   {clock gene mRNA}
 
 Protein degradation [clock protein] → ;  
 
 Transcriptional repressor synthesis  → [Transcriptional repressor];   {clock protein}
 
 Transcriptional repressor degradation [Transcriptional repressor] → ;  
 
 Neuropeptide synthesis  → [Neuropeptide];   {clock gene mRNA}
 
 Neuropeptide degradation [Neuropeptide] → ;  
 
Rules (1)
 
 Assignment Rule (name: F) F = 1/2*(V1+V2)
 
 Cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 clock gene mRNA
Compartment: Cell
Initial concentration: 4.25
 
 clock protein
Compartment: Cell
Initial concentration: 3.25
 
   Transcriptional repressor
Compartment: Cell
Initial concentration: 2.25
 
 Neuropeptide
Compartment: Cell
Initial concentration: 2.5
 
 clock gene mRNA
Compartment: Cell
Initial concentration: 0.0
 
 clock protein
Compartment: Cell
Initial concentration: 0.0
 
   Transcriptional repressor
Compartment: Cell
Initial concentration: 0.0
 
 Neuropeptide
Compartment: Cell
Initial concentration: 0.0
 
Global Parameters (19)
 
   F  
 
   v_1
Value: 6.8355   (Units: nM_hr_1)
Constant
 
   K1
Value: 2.7266   (Units: nM)
Constant
 
   n
Value: 5.6645   (Units: dimensionless)
Constant
 
   v_2
Value: 8.4297   (Units: nM_hr_1)
Constant
 
   K2
Value: 0.291   (Units: nM)
Constant
 
   vc
Value: 6.7924   (Units: nM_hr_1)
Constant
 
   K
Value: 1.0   (Units: dimensionless)
Constant
 
   Kc
Value: 4.8283   (Units: nM)
Constant
 
   L
Constant
 
   k3
Value: 0.1177   (Units: hr_1)
Constant
 
   v_4
Value: 1.0841   (Units: nM_hr_1)
Constant
 
   K4
Value: 8.1343   (Units: nM)
Constant
 
   k5
Value: 0.3352   (Units: hr_1)
Constant
 
   v_6
Value: 4.6645   (Units: nM_hr_1)
Constant
 
   K6
Value: 9.9849   (Units: nM)
Constant
 
   k7
Value: 0.2282   (Units: hr_1)
Constant
 
   v_8
Value: 3.5216   (Units: nM_hr_1)
Constant
 
   K8
Value: 7.4519   (Units: nM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000185

Curator's comment: (updated: 20 Aug 2008 20:44:41 BST)

The plot corresponds to Fig 2A of the paper. Results obtained using MathSBML.

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