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BIOMD0000000025 - Smolen2002_CircClock

 

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Reference Publication
Publication ID: 12414672
Smolen P, Baxter DA, Byrne JH.
A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator.
Biophys. J. 2002 Nov; 83(5): 2349-2359
Department of Neurobiology and Anatomy, W. M. Keck Center for the Neurobiology of Learning and Memory, The University of Texas-Houston Medical School, Houston, TX 77225, USA.  [more]
Model
Original Model: BIOMD0000000025.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6618294363
Submission Date: 13 Sep 2005 13:31:54 UTC
Last Modification Date: 15 May 2012 21:41:34 UTC
Creation Date: 29 Jun 2005 11:01:49 UTC
Encoders:  Nicolas Le Novère
set #1
bqmodel:isDerivedFrom PubMed 11517254
set #2
bqbiol:is KEGG Pathway dme04710
bqbiol:isVersionOf Gene Ontology circadian rhythm
set #3
bqbiol:hasTaxon Taxonomy Drosophila melanogaster
Notes

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 12414672 Submission Date: 13 Sep 2005 13:31:54 UTC Last Modification Date: 15 May 2012 21:41:34 UTC Creation Date: 29 Jun 2005 11:01:49 UTC
Mathematical expressions
Reactions
Per production dClk production Per degradation dClk degradation
Rules
Assignment Rule (variable: free dClk) Assignment Rule (variable: dClkF_tau1) Assignment Rule (variable: dClkF_tau2)  
Physical entities
Compartments Species
CELL EmptySet Per dClk
free dClk    
Global parameters
dClkF_tau1 dClkF_tau2 tau1 tau2
Vsp K1 Vsc K2
kdc kdp    
Reactions (4)
 
 Per production [EmptySet] → [Per];   {free dClk}
 
 dClk production [EmptySet] → [dClk];   {free dClk}
 
 Per degradation [Per] → [EmptySet];  
 
 dClk degradation [dClk] → [EmptySet];  
 
Rules (3)
 
 Assignment Rule (name: dClkF) free dClk = piecewise(0, dClk-Per < 0, dClk-Per)
 
 Assignment Rule (name: dClkF_tau1) dClkF_tau1 = piecewise(0, delay(dClk, tau1)-delay(Per, tau1) < 0, delay(dClk, tau1)-delay(Per, tau1))
 
 Assignment Rule (name: dClkF_tau2) dClkF_tau2 = piecewise(0, delay(dClk, tau2)-delay(Per, tau2) < 0, delay(dClk, tau2)-delay(Per, tau2))
 
  Spatial dimensions: 3.0  Compartment size: 1.0E-15
 
   EmptySet
Compartment: CELL
Initial concentration: 0.0
Constant
 
 Per
Compartment: CELL
Initial concentration: 5.0E-16
 
 dClk
Compartment: CELL
Initial concentration: 1.0E-16
 
  free dClk
Compartment: CELL
Initial concentration: 0.0
 
Global Parameters (10)
 
  dClkF_tau1
Value: NaN   (Units: nM)
 
  dClkF_tau2
Value: NaN   (Units: nM)
 
   tau1
Value: 10.0   (Units: hour (new default))
Constant
 
   tau2
Value: 10.0   (Units: hour (new default))
Constant
 
   Vsp
Value: 0.5   (Units: nM_per_hr)
Constant
 
   K1
Value: 0.3   (Units: nM)
Constant
 
   Vsc
Value: 0.25   (Units: nM_per_hr)
Constant
 
   K2
Value: 0.1   (Units: nM)
Constant
 
   kdc
Value: 0.5   (Units: per_hr)
Constant
 
   kdp
Value: 0.5   (Units: per_hr)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000025

Curator's comment: (updated: 22 Sep 2010 11:17:42 BST)

Reproduction of figure 1 of the original publication using octave.

To simulate this model, the sbml file first was translated to matlab using the SBW online translator (http://sys-bio.org/SBMLTranslator/). A function to intra- and extrapolate the delayed variables was added and the time course simulated using ode23. The changes to the code and detailed instruction on how to perform the simulations are available on demand, and, hopefully soon, from our FAQ.

As the initial conditions are not known, the time course is different from the published results for the first 15 hours and the oscillations are shifted.

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