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BIOMD0000000308 - Tyson2003_NegFB_Oscillator

 

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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: BIOMD0000000308.origin
Submitter: Lukas Endler
Submission ID: MODEL1102100004
Submission Date: 10 Feb 2011 03:15:42 UTC
Last Modification Date: 06 Apr 2014 20:03:14 UTC
Creation Date: 10 Feb 2011 03:49:32 UTC
Encoders:  Lukas Endler
   John J Tyson
set #1
bqbiol:hasTaxon Taxonomy cellular organisms
set #2
bqbiol:isVersionOf Gene Ontology regulation of binding
set #3
bqbiol:hasPart Gene Ontology intracellular protein kinase cascade
set #4
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

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

This is an SBML implementation the model of negative feedback oscillator (figure 2a) 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 03:15:42 UTC Last Modification Date: 06 Apr 2014 20:03:14 UTC Creation Date: 10 Feb 2011 03:49:32 UTC
Mathematical expressions
Reactions
r1 r2 r3 r4
r5 r6    
Rules
Assignment Rule (variable: Y) Assignment Rule (variable: R)    
Physical entities
Compartments Species
env Rp X Yp
S Y R
Global parameters
k0 k1 k2 k2_prime
k3 Yt Km3 k4
Km4 k5 Rt Km5
k6 Km6    
Reactions (6)
 
 r1  → [X];   {S}
 
 r2 [X] → ;   {Rp}
 
 r3 [Y] → [Yp];   {X}
 
 r4 [Yp] → [Y];  
 
 r5 [R] → [Rp];   {Yp}
 
 r6 [Rp] → [R];  
 
Rules (2)
 
 Assignment Rule (name: Y) Y = Yt-Yp
 
 Assignment Rule (name: R) R = Rt-Rp
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Rp
Compartment: env
Initial concentration: 0.0
 
 X
Compartment: env
Initial concentration: 0.0
 
 Yp
Compartment: env
Initial concentration: 0.0
 
 S
Compartment: env
Initial concentration: 0.0
 
  Y
Compartment: env
 
  R
Compartment: env
 
Global Parameters (14)
 
 k0
Constant
 
 k1
Value: 1.0   (Units: per_s)
Constant
 
 k2
Value: 0.01   (Units: per_s)
Constant
 
 k2_prime
Value: 10.0   (Units: per_M_per_s)
Constant
 
 k3
Value: 0.1   (Units: per_s)
Constant
 
 Yt
Value: 1.0   (Units: M)
Constant
 
 Km3
Value: 0.01   (Units: M)
Constant
 
 k4
Value: 0.2   (Units: M_per_s)
Constant
 
 Km4
Value: 0.01   (Units: M)
Constant
 
 k5
Value: 0.1   (Units: per_s)
Constant
 
 Rt
Value: 1.0   (Units: M)
Constant
 
 Km5
Value: 0.01   (Units: M)
Constant
 
 k6
Value: 0.05   (Units: M_per_s)
Constant
 
 Km6
Value: 0.01   (Units: M)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000308

Curator's comment: (updated: 10 Feb 2011 03:48:11 GMT)

Bifurcation diagram as in fig 2a of the original publication. the steady state (blue stable: thick line, instable: dashed) and the maximal and minimal oscillatory concentrations (steel blue dotted) of Rp are plotted against varying input values of S. The diagram was created using Oscill8 v 2.0.1 with the ode version of the model automatically generated by the SBW converter.

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