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BIOMD0000000034 - Smolen2004_CircClock

 

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Reference Publication
Publication ID: 15111397
Smolen P, Hardin PE, Lo BS, Baxter DA, Byrne JH.
Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK.
Biophys. J. 2004 May; 86(5): 2786-2802
Department of Neurobiology and Anatomy, W M Keck Center for the Neurobiology of Learning and Memory, The University of Texas-Houston Medical School, Houston, Texas 77225, USA.  [more]
Model
Original Model: BIOMD0000000034.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6619579403
Submission Date: 13 Sep 2005 13:53:25 UTC
Last Modification Date: 05 Jul 2012 14:42:52 UTC
Creation Date: 24 Jun 2005 12:05:27 UTC
Encoders:  Nicolas Le Novère
set #1
bqbiol:isVersionOf Gene Ontology circadian rhythm
set #2
bqbiol:is KEGG Pathway dme04710
bqbiol:occursIn Taxonomy Drosophila melanogaster
Notes

No inititial conditions are specified in the paper. Because there is a basal rate of transcription for each gene, it doesn't matter much. With the agreement of Paul Smolen, I put all the initial concentration at 0.001 nanomoles. N Le Novère.


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: 15111397 Submission Date: 13 Sep 2005 13:53:25 UTC Last Modification Date: 05 Jul 2012 14:42:52 UTC Creation Date: 24 Jun 2005 12:05:27 UTC
Mathematical expressions
Reactions
Per production Vri production Pdp production Clk production
Clk specific degradation Pdp specific degradation Vri specific degradation first cytoplasmic Per phosphorylation
second cytoplasmic Per phosphorylation Per nuclear transport first nuclear Per phosphorylation second nuclear Rer phosphorylation
Per specific degradation Clk aspecific degradation Pdp aspecific degradation Vri aspecific degradation
Per_cyt aspecific degradation Per-P_cyt aspecific degradation Per-PP_cyt aspecific degradation Per_nuc aspecific degradation
Per-P_nuc aspecific degradation Per-PP_nuc aspecific degradation    
Rules
Rate Rule (variable: ACvri) Rate Rule (variable: ACper) Rate Rule (variable: ACpdp) Rate Rule (variable: OPvri)
Rate Rule (variable: OPper) Rate Rule (variable: OPpdp)    
Physical entities
Compartments Species
cytoplasm P0cyt P1cyt P2cyt
     
nucleus P0nuc P1nuc P2nuc
VRI CLK PDP
Global parameters
ACvri ACper ACpdp Kpv
Kpp Kppd Kvc Kpdc
Kcv Kcp Kcpd Kvdeac
Kpdeac Kpddeac Fv Fp
Fpd OPvri OPper OPpdp
Tvriop Tperop Tpdpop N
Vper Vvri Vpdp Vclk
Rpbas Rvbas Rcbas Rpdbas
Vdclk vdvri vdpdp Tdelay
Vpcyt Kpcyt Vpnuc Kpnuc
Vtrans Ktrans Vdegp Kdegp
kd      
Reactions (22)
 
 Per production  → [P0cyt];  
 
 Vri production  → [VRI];  
 
 Pdp production  → [PDP];  
 
 Clk production  → [CLK];   {PDP} , {VRI}
 
 Clk specific degradation [CLK] → ;  
 
 Pdp specific degradation [PDP] → ;  
 
 Vri specific degradation [VRI] → ;  
 
 first cytoplasmic Per phosphorylation [P0cyt] → [P1cyt];  
 
 second cytoplasmic Per phosphorylation [P1cyt] → [P2cyt];  
 
 Per nuclear transport [P2cyt] → [P0nuc];  
 
 first nuclear Per phosphorylation [P0nuc] → [P1nuc];  
 
 second nuclear Rer phosphorylation [P1nuc] → [P2nuc];  
 
 Per specific degradation [P2nuc] → ;  
 
 Clk aspecific degradation [CLK] → ;  
 
 Pdp aspecific degradation [PDP] → ;  
 
 Vri aspecific degradation [VRI] → ;  
 
 Per_cyt aspecific degradation [P0cyt] → ;  
 
 Per-P_cyt aspecific degradation [P1cyt] → ;  
 
 Per-PP_cyt aspecific degradation [P2cyt] → ;  
 
 Per_nuc aspecific degradation [P0nuc] → ;  
 
 Per-P_nuc aspecific degradation [P1nuc] → ;  
 
 Per-PP_nuc aspecific degradation [P2nuc] → ;  
 
Rules (6)
 
 Rate Rule (name: parameter_0000001) d [ ACvri] / d t= parameter_0000017*species_0000008/(species_0000008+parameter_0000011)*parameter_0000005/(parameter_0000005+species_0000001+species_0000002+species_0000003)*(1-parameter_0000001)-parameter_0000014*parameter_0000001
 
 Rate Rule (name: parameter_0000002) d [ ACper] / d t= parameter_0000018*species_0000008/(species_0000008+parameter_0000012)*parameter_0000006/(parameter_0000006+species_0000001+species_0000002+species_0000003)*(1-parameter_0000002)-parameter_0000015*parameter_0000002
 
 Rate Rule (name: parameter_0000003) d [ ACpdp] / d t= parameter_0000019*species_0000008/(species_0000008+parameter_0000013)*parameter_0000007/(parameter_0000007+species_0000001+species_0000002+species_0000003)*(1-parameter_0000003)-parameter_0000016*parameter_0000003
 
 Rate Rule (name: parameter_0000020) d [ OPvri] / d t= (parameter_0000001^parameter_0000026-parameter_0000020)/parameter_0000023
 
 Rate Rule (name: parameter_0000021) d [ OPper] / d t= (parameter_0000002^parameter_0000026-parameter_0000021)/parameter_0000024
 
 Rate Rule (name: parameter_0000022) d [ OPpdp] / d t= (parameter_0000003^parameter_0000026-parameter_0000022)/parameter_0000025
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 P0cyt
Compartment: cytoplasm
Initial concentration: 0.0010
 
 P1cyt
Compartment: cytoplasm
Initial concentration: 0.0010
 
 P2cyt
Compartment: cytoplasm
Initial concentration: 0.0010
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 P0nuc
Compartment: nucleus
Initial concentration: 0.0010
 
 P1nuc
Compartment: nucleus
Initial concentration: 0.0010
 
 P2nuc
Compartment: nucleus
Initial concentration: 0.0010
 
 VRI
Compartment: nucleus
Initial concentration: 0.0010
 
 CLK
Compartment: nucleus
Initial concentration: 0.0010
 
 PDP
Compartment: nucleus
Initial concentration: 0.0010
 
Global Parameters (45)
 
   ACvri
Value: NaN
 
   ACper
Value: NaN
 
   ACpdp
Value: NaN
 
   Kpv
Value: 0.2
Constant
 
   Kpp
Value: 0.24
Constant
 
   Kppd
Value: 0.1
Constant
 
   Kvc
Value: 0.54
Constant
 
   Kpdc
Value: 0.54
Constant
 
   Kcv
Value: 0.083
Constant
 
   Kcp
Value: 0.134
Constant
 
   Kcpd
Value: 0.248
Constant
 
   Kvdeac
Value: 0.2124
Constant
 
   Kpdeac
Value: 0.2124
Constant
 
   Kpddeac
Value: 0.2124
Constant
 
   Fv
Value: 1.062
Constant
 
   Fp
Value: 1.062
Constant
 
   Fpd
Value: 1.062
Constant
 
   OPvri
Value: NaN
 
   OPper
Value: NaN
 
   OPpdp
Value: NaN
 
   Tvriop
Value: 2.8249
Constant
 
   Tperop
Value: 2.8249
Constant
 
   Tpdpop
Value: 2.8249
Constant
 
   N
Value: 5.0
Constant
 
   Vper
Value: 10.62
Constant
 
   Vvri
Value: 76.464
Constant
 
   Vpdp
Value: 344.09
Constant
 
   Vclk
Value: 1.062
Constant
 
   Rpbas
Value: 0.02124
Constant
 
   Rvbas
Value: 0.19116
Constant
 
   Rcbas
Value: 0.001062
Constant
 
   Rpdbas
Value: 0.38232
Constant
 
   Vdclk
Value: 0.2124
Constant
 
   vdvri
Value: 0.7434
Constant
 
   vdpdp
Value: 0.6903
Constant
 
   Tdelay
Value: 2.8249
Constant
 
   Vpcyt
Value: 1.6992
Constant
 
   Kpcyt
Value: 0.25
Constant
 
   Vpnuc
Value: 0.3186
Constant
 
   Kpnuc
Value: 0.0010
Constant
 
   Vtrans
Value: 1.6992
Constant
 
   Ktrans
Value: 0.25
Constant
 
   Vdegp
Value: 5.31
Constant
 
   Kdegp
Value: 0.01
Constant
 
   kd
Value: 0.00531
Constant
 
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