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BIOMD0000000307 - Tyson2003_Substrate_Depletion_Osc

 

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Reference Publication
Publication ID: 12648679
Tyson JJ, Chen KC, Novak B.
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.
Curr. Opin. Cell Biol. 2003 Apr; 15(2): 221-231
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. tyson@vt.edu  [more]
Model
Original Model: BIOMD0000000307.xml.origin
Submitter: Lukas Endler
Submission ID: MODEL1102100006
Submission Date: 10 Feb 2011 03:31:14 UTC
Last Modification Date: 20 Apr 2012 22:02:17 UTC
Creation Date: 10 Feb 2011 03:49:02 UTC
Encoders:  Lukas Endler
set #1
bqbiol:hasTaxon Taxonomy cellular organisms
set #2
bqbiol:isVersionOf Gene Ontology regulation of binding
set #3
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

This is an SBML implementation the model of the substrate depletion oscillator (figure 2c) described in the article:
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.
Tyson JJ, Chen KC, Novak B. Curr Opin Cell Biol. 2003 Apr;15(2):221-31. PubmedID:12648679; DOI:10.1016/S0955-0674(03)00017-6;

Abstract:
The physiological responses of cells to external and internal stimuli are governed by genes and proteins interacting in complex networks whose dynamical properties are impossible to understand by intuitive reasoning alone. Recent advances by theoretical biologists have demonstrated that molecular regulatory networks can be accurately modeled in mathematical terms. These models shed light on the design principles of biological control systems and make predictions that have been verified experimentally.

Originally created by libAntimony v1.4 (using libSBML 3.4.1)

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
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: 12648679 Submission Date: 10 Feb 2011 03:31:14 UTC Last Modification Date: 20 Apr 2012 22:02:17 UTC Creation Date: 10 Feb 2011 03:49:02 UTC
Mathematical expressions
Reactions
r0 r1 r2 r3
r4      
Rules
Assignment Rule (variable: Km3) Assignment Rule (variable: Km4) Assignment Rule (variable: Ep) Assignment Rule (variable: E)
Physical entities
Compartments Species
env R X S
Ep E  
Global parameters
k0_prime k0 k1 k2
k3 J3 k4 J4
Et Km3 Km4  
Reactions (5)
 
 r0 [X] → [R];   {Ep}
 
 r1  → [X];   {S}
 
 r2 [R] → ;  
 
 r3 [E] → [Ep];   {R}
 
 r4 [Ep] → [E];  
 
Rules (4)
 
 Assignment Rule (name: Km3) Km3 = J3*Et
 
 Assignment Rule (name: Km4) Km4 = J4*Et
 
 Assignment Rule (name: Ep) Ep = goldbeter_koshland(k3*R, k4, J3, J4)*Et
 
 Assignment Rule (name: E) E = Et-Ep
 
Functions (1)
 
 goldbeter_koshland lambda(v1, v2, J1, J2, 2*v1*J2/(v2-v1+J1*v2+J2*v1+((v2-v1+J1*v2+J2*v1)^2-4*(v2-v1)*v1*J2)^(1/2)))
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 R
Compartment: env
Initial concentration: 0.0
 
 X
Compartment: env
Initial concentration: 0.0
 
 S
Compartment: env
Initial concentration: 0.0
 
  Ep
Compartment: env
 
  E
Compartment: env
 
Global Parameters (11)
 
 k0_prime
Value: 0.01   (Units: per_s)
Constant
 
 k0
Value: 0.4   (Units: per_M_per_s)
Constant
 
 k1
Value: 1.0   (Units: per_s)
Constant
 
 k2
Value: 1.0   (Units: per_s)
Constant
 
 k3
Value: 1.0   (Units: per_s)
Constant
 
 J3
Value: 0.05   (Units: dimensionless)
Constant
 
 k4
Value: 0.3   (Units: M_per_s)
Constant
 
 J4
Value: 0.05   (Units: dimensionless)
Constant
 
 Et
Value: 1.0   (Units: M)
Constant
 
  Km3
Value: NaN   (Units: M)
 
  Km4
Value: NaN   (Units: M)
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000307

Curator's comment: (updated: 10 Feb 2011 03:45:09 GMT)

Bifurcation diagram as in fig 2c of the original publication. the steady state (stable: thick line, instable: dashed) and the maximal and minimal oscillatory concentrations (circles) of R are plotted against varying input values of S. The diagram was created using XPP with the xpp version of the model automatically generated by the BioModels.net converter.

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