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BIOMD0000000022 - Ueda2001_CircClock

 

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Reference Publication
Publication ID: 11403560
Ueda HR, Hagiwara M, Kitano H.
Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm.
J. Theor. Biol. 2001 Jun; 210(4): 401-406
ERATO Kitano Symbiotic Systems Group, Suite 6A, M31, 6-31-15 Jinguumae, Shibuya, Tokyo, 150-0001, Japan. hiro@m.u-tokyo.ac.jp  [more]
Model
Original Model: BIOMD0000000022.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6617909980
Submission Date: 13 Sep 2005 13:25:30 UTC
Last Modification Date: 26 Mar 2014 16:51:09 UTC
Creation Date: 21 Sep 2005 17:16:35 UTC
Encoders:  Nicolas Le Novère
   Bruce Shapiro
set #1
bqbiol:isVersionOf KEGG Pathway dme04710
Gene Ontology circadian rhythm
set #2
bqbiol:hasTaxon Taxonomy Drosophila melanogaster
set #3
bqmodel:isDerivedFrom PubMed 10531060
Notes

Bruce Shapiro: Generated by Cellerator Version 1.0 update 3.0303 using Mathematica 4.1 for Microsoft Windows (June 13, 2001), April 2, 2003 16:49:13, using (PC,x86, Microsoft Windows,WindowsNT,Windows)

Bruce Shapiro: Corrected 29 March 2005

Nicolas Le Novère: Added Dbt and Cyc species, and the corresponding reactions. 23 April 2005


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: 11403560 Submission Date: 13 Sep 2005 13:25:30 UTC Last Modification Date: 26 Mar 2014 16:51:09 UTC Creation Date: 21 Sep 2005 17:16:35 UTC
Mathematical expressions
Reactions
Per transcription non-specific Per mRNA degradation Tim transcription non-specific Tim mRNA degradation
Clk transcription non-specific Clk mRNA degradation Clk-Cyc nuclear import Clk-Cyc nuclear export
Per-Tim nuclear export Per-Tim nuclear import Clk Cyc equilibrium Per Tim equilibrium
Tim translation Clk translation Per translation non-specific Per_cyt degradation
non-specific Per-Tim_cyt degradation non-specific Per-Tim_nuc degradation non-specific Clk-Cyc_cyt degradation non-specific Clk_cyt degradation
non-specific Clk-Cyc_nuc degradation non-specific Tim_cyt degradation Per mRNA degradation Dbt regulated Per_cyt degradation
Tim mRNA degradation Tim_cyt degradation Per-Tim_cyt degradation Per-Tim_nuc degradation
Clk mRNA degradation Clk_cyt degradation Clk-Cyc_cyt degradation Reaction37
Physical entities
Compartments Species
Drosophilia EmptySet    
cytoplasm Clk-Cyc_cyt Clk_cyt Clk_mRNA
Per_cyt Per_mRNA Per-Tim_cyt
Tim_cyt Tim_mRNA Cyc_cyt
Dbt_cyt    
nucleus Clk-Cyc_nuc Per-Tim_nuc  
Reactions (32)
 
 Per transcription [EmptySet] → [Per_mRNA];   {Clk-Cyc_nuc} , {Per-Tim_nuc}
 
 non-specific Per mRNA degradation [Per_mRNA] → [EmptySet];  
 
 Tim transcription [EmptySet] → [Tim_mRNA];   {Clk-Cyc_nuc} , {Per-Tim_nuc}
 
 non-specific Tim mRNA degradation [Tim_mRNA] → [EmptySet];  
 
 Clk transcription [EmptySet] → [Clk_mRNA];   {Per-Tim_nuc} , {Clk-Cyc_nuc}
 
 non-specific Clk mRNA degradation [Clk_mRNA] → [EmptySet];  
 
 Clk-Cyc nuclear import [Clk-Cyc_cyt] → [Clk-Cyc_nuc];  
 
 Clk-Cyc nuclear export [Clk-Cyc_nuc] → [Clk-Cyc_cyt];  
 
 Per-Tim nuclear export [Per-Tim_nuc] → [Per-Tim_cyt];  
 
 Per-Tim nuclear import [Per-Tim_cyt] → [Per-Tim_nuc];  
 
 Clk Cyc equilibrium [Cyc_cyt] + [Clk_cyt] ↔ [Clk-Cyc_cyt];  
 
 Per Tim equilibrium [Per_cyt] + [Tim_cyt] ↔ [Per-Tim_cyt];  
 
 Tim translation [EmptySet] → [Tim_cyt];   {Tim_mRNA}
 
 Clk translation [EmptySet] → [Clk_cyt];   {Clk_mRNA}
 
 Per translation [EmptySet] → [Per_cyt];   {Per_mRNA}
 
 non-specific Per_cyt degradation [Per_cyt] → [EmptySet];  
 
 non-specific Per-Tim_cyt degradation [Per-Tim_cyt] → [EmptySet];  
 
 non-specific Per-Tim_nuc degradation [Per-Tim_nuc] → [EmptySet];  
 
 non-specific Clk-Cyc_cyt degradation [Clk-Cyc_cyt] → [EmptySet];  
 
 non-specific Clk_cyt degradation [Clk_cyt] → [EmptySet];  
 
 non-specific Clk-Cyc_nuc degradation [Clk-Cyc_nuc] → [EmptySet];  
 
 non-specific Tim_cyt degradation [Tim_cyt] → [EmptySet];  
 
 Per mRNA degradation [Per_mRNA] → [EmptySet];  
 
 Dbt regulated Per_cyt degradation [Per_cyt] → [EmptySet];   {Dbt_cyt}
 
 Tim mRNA degradation [Tim_mRNA] → [EmptySet];  
 
 Tim_cyt degradation [Tim_cyt] → [EmptySet];  
 
 Per-Tim_cyt degradation [Per-Tim_cyt] → [EmptySet];  
 
 Per-Tim_nuc degradation [Per-Tim_nuc] → [EmptySet];  
 
 Clk mRNA degradation [Clk_mRNA] → [EmptySet];  
 
 Clk_cyt degradation [Clk_cyt] → [EmptySet];  
 
 Clk-Cyc_cyt degradation [Clk-Cyc_cyt] → [EmptySet];  
 
 Reaction37 [Clk-Cyc_nuc] → [EmptySet];  
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
   EmptySet
Compartment: Drosophilia
Initial amount: 0.0
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 Clk-Cyc_cyt
Compartment: cytoplasm
Initial amount: 0.3
 
 Clk_cyt
Compartment: cytoplasm
Initial amount: 0.2
 
 Clk_mRNA
Compartment: cytoplasm
Initial amount: 0.1
 
 Per_cyt
Compartment: cytoplasm
Initial amount: 0.6
 
 Per_mRNA
Compartment: cytoplasm
Initial amount: 0.5
 
 Per-Tim_cyt
Compartment: cytoplasm
Initial amount: 0.9
 
 Tim_cyt
Compartment: cytoplasm
Initial amount: 0.8
 
 Tim_mRNA
Compartment: cytoplasm
Initial amount: 0.7
 
 Cyc_cyt
Compartment: cytoplasm
Initial amount: 1.0
Constant
 
 Dbt_cyt
Compartment: cytoplasm
Initial amount: 1.0
Constant
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 Clk-Cyc_nuc
Compartment: nucleus
Initial amount: 0.4
 
 Per-Tim_nuc
Compartment: nucleus
Initial amount: 1.0
 
Per transcription (7)
 
   a
Value: 1.0
Constant
 
   A1
Value: 0.45
Constant
 
   B1
Constant
 
   C1
Constant
 
   R1
Value: 1.02
Constant
 
   S1
Value: 1.45
Constant
 
   r
Value: 4.0
Constant
 
non-specific Per mRNA degradation (1)
 
   D0
Value: 0.012
Constant
 
Tim transcription (7)
 
   a
Value: 1.0
Constant
 
   A2
Value: 0.45
Constant
 
   B2
Constant
 
   C2
Constant
 
   R2
Value: 1.02
Constant
 
   S3
Value: 1.45
Constant
 
   r
Value: 4.0
Constant
 
non-specific Tim mRNA degradation (1)
 
   D0
Value: 0.012
Constant
 
Clk transcription (7)
 
   a
Value: 1.0
Constant
 
   A3
Value: 0.8
Constant
 
   B3
Value: 0.6
Constant
 
   C3
Constant
 
   R3
Value: 0.89
Constant
 
   S5
Value: 1.63
Constant
 
   r
Value: 4.0
Constant
 
non-specific Clk mRNA degradation (1)
 
   D0
Value: 0.012
Constant
 
Clk-Cyc nuclear import (2)
 
   K3
Value: 2.0
Constant
 
   T3
Value: 1.63
Constant
 
Clk-Cyc nuclear export (2)
 
   k4
Value: 2.0
Constant
 
   T4
Value: 0.52
Constant
 
Per-Tim nuclear export (2)
 
   K2
Value: 2.0
Constant
 
   T2
Value: 0.72
Constant
 
Per-Tim nuclear import (2)
 
   K1
Value: 2.0
Constant
 
   T1
Value: 1.73
Constant
 
Clk Cyc equilibrium (2)
 
   V3
Value: 1.63
Constant
 
   V4
Value: 1.63
Constant
 
Per Tim equilibrium (2)
 
   V1
Value: 1.45
Constant
 
   V2
Value: 1.45
Constant
 
Tim translation (1)
 
   S4
Value: 0.48
Constant
 
Clk translation (1)
 
   S6
Value: 0.47
Constant
 
Per translation (1)
 
   S2
Value: 0.48
Constant
 
non-specific Per_cyt degradation (1)
 
   D0
Value: 0.012
Constant
 
non-specific Per-Tim_cyt degradation (1)
 
   D0
Value: 0.012
Constant
 
non-specific Per-Tim_nuc degradation (1)
 
   D0
Value: 0.012
Constant
 
non-specific Clk-Cyc_cyt degradation (1)
 
   D0
Value: 0.012
Constant
 
non-specific Clk_cyt degradation (1)
 
   D0
Value: 0.012
Constant
 
non-specific Clk-Cyc_nuc degradation (1)
 
   D0
Value: 0.012
Constant
 
non-specific Tim_cyt degradation (1)
 
   D0
Value: 0.012
Constant
 
Per mRNA degradation (2)
 
   D1
Value: 0.94
Constant
 
   L1
Value: 0.3
Constant
 
Dbt regulated Per_cyt degradation (2)
 
   D2
Value: 0.44
Constant
 
   L2
Value: 0.2
Constant
 
Tim mRNA degradation (2)
 
   D3
Value: 0.94
Constant
 
   L3
Value: 0.3
Constant
 
Tim_cyt degradation (2)
 
   D4
Value: 0.44
Constant
 
   L4
Value: 0.2
Constant
 
Per-Tim_cyt degradation (2)
 
   D5
Value: 0.44
Constant
 
   L5
Value: 0.2
Constant
 
Per-Tim_nuc degradation (2)
 
   D6
Value: 0.29
Constant
 
   L6
Value: 0.2
Constant
 
Clk mRNA degradation (2)
 
   D7
Value: 0.54
Constant
 
   L7
Value: 0.13
Constant
 
Clk_cyt degradation (2)
 
   D8
Value: 0.6
Constant
 
   L8
Value: 0.2
Constant
 
Clk-Cyc_cyt degradation (2)
 
   D9
Value: 0.6
Constant
 
   L9
Value: 0.2
Constant
 
Reaction37 (2)
 
   D10
Value: 0.3
Constant
 
   L10
Value: 0.2
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000022

Curator's comment: (updated: 19 Oct 2006 22:05:48 BST)

Figure 3d reproduced by COPASI 4 build 19

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