BioModels Database logo

BioModels Database

spacer

BIOMD0000000058 - Bindschadler2001_coupled_Ca_oscillators

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 12779457
Bindschadler M, Sneyd J.
A bifurcation analysis of two coupled calcium oscillators.
Chaos 2001 Mar; 11(1): 237-246
Department of Mathematics, University of Michigan, Ann Arbor, Michigan.  [more]
Model
Original Model: BIOMD0000000058.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL9107330008
Submission Date: 08 Jun 2006 08:06:22 UTC
Last Modification Date: 24 May 2014 16:17:03 UTC
Creation Date: 31 May 2006 08:28:41 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasTaxon Taxonomy Rattus norvegicus
bqbiol:hasPart Gene Ontology inositol phosphate-mediated signaling
Gene Ontology calcium-mediated signaling
bqbiol:is KEGG Pathway map04020
set #2
bqmodel:isDerivedFrom BioModels Database LeBeau1999_IP3R_Phosphorylation
set #3
bqbiol:occursIn Brenda Tissue Ontology BTO:0000028
Notes

The model reproduces the same amplitude antiphase calcium oscillations of coupled cells depicted in Figure 5B of the publication. This model was successfully tested on Jarnac and MathSBML. The values of "h1" and "h2" are not given in the publication, but the antiphase oscillations are reproduced over a narrow range of values of h1, h2,c1,c2,D and p. The values of D and p are given, while the other values were plugged in, in order to simulate the time profiles shown in the Figure. The time t=0 in the figure may have been fixed after the system was allowed to settle, and hence does not correspond to the t=0 of the simulation.


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: 12779457 Submission Date: 08 Jun 2006 08:06:22 UTC Last Modification Date: 24 May 2014 16:17:03 UTC Creation Date: 31 May 2006 08:28:41 UTC
Mathematical expressions
Reactions
IP3R mediated Ca release Cell1 ATPase pump mediated Ca efflux Cell1 IP3R independent Ca release Cell1 Inactivated to Shut state transition Cell1
Open to Inactivated state transition Cell1 IP3R mediated Ca release Cell2 ATPase pump mediated Ca efflux Cell2 IP3R independent Ca release Cell2
Inactivated to Shut state transition Cell2 Open to Inactivated state transition Cell2 Diffusion of Ca between cells  
Rules
Assignment Rule (variable: Phi1_c1) Assignment Rule (variable: Phi_minus1_c1) Assignment Rule (variable: Phi2_c1) Assignment Rule (variable: Phi3_c1)
Assignment Rule (variable: Phi1_c2) Assignment Rule (variable: Phi_minus1_c2) Assignment Rule (variable: Phi2_c2) Assignment Rule (variable: Phi3_c2)
Physical entities
Compartments Species
compartment Calcium ion Cell1 Receptor fraction Cell1 Calcium ion Cell2
Receptor fraction Cell2    
Global parameters
Phi1_c1 r2 R1 Phi_minus1_c1
k1 R3 Phi2_c1 k2
r4 Phi3_c1 k3 R5
Phi1_c2 Phi_minus1_c2 Phi2_c2 Phi3_c2
Reactions (11)
 
 IP3R mediated Ca release Cell1  → [Calcium ion Cell1];   {Receptor fraction Cell1}
 
 ATPase pump mediated Ca efflux Cell1 [Calcium ion Cell1] → ;  
 
 IP3R independent Ca release Cell1  → [Calcium ion Cell1];  
 
 Inactivated to Shut state transition Cell1  → [Receptor fraction Cell1];  
 
 Open to Inactivated state transition Cell1 [Receptor fraction Cell1] → ;  
 
 IP3R mediated Ca release Cell2  → [Calcium ion Cell2];   {Receptor fraction Cell2}
 
 ATPase pump mediated Ca efflux Cell2 [Calcium ion Cell2] → ;  
 
 IP3R independent Ca release Cell2  → [Calcium ion Cell2];  
 
 Inactivated to Shut state transition Cell2  → [Receptor fraction Cell2];  
 
 Open to Inactivated state transition Cell2 [Receptor fraction Cell2] → ;  
 
 Diffusion of Ca between cells [Calcium ion Cell2] → [Calcium ion Cell1];  
 
Rules (8)
 
 Assignment Rule (name: Phi1_c1) Phi1_c1 = r2*c1/(R1+c1)
 
 Assignment Rule (name: Phi_minus1_c1) Phi_minus1_c1 = k1/(R3+c1)
 
 Assignment Rule (name: Phi2_c1) Phi2_c1 = (k2+r4*c1)/(R3+c1)
 
 Assignment Rule (name: Phi3_c1) Phi3_c1 = k3/(R5+c1)
 
 Assignment Rule (name: Phi1_c2) Phi1_c2 = r2*c2/(R1+c2)
 
 Assignment Rule (name: Phi_minus1_c2) Phi_minus1_c2 = k1/(R3+c2)
 
 Assignment Rule (name: Phi2_c2) Phi2_c2 = (k2+r4*c2)/(R3+c2)
 
 Assignment Rule (name: Phi3_c2) Phi3_c2 = k3/(R5+c2)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Calcium ion Cell1
Compartment: compartment
Initial concentration: 0.3
 
 Receptor fraction Cell1
Compartment: compartment
Initial concentration: 0.8
 
 Calcium ion Cell2
Compartment: compartment
Initial concentration: 0.1
 
 Receptor fraction Cell2
Compartment: compartment
Initial concentration: 0.1
 
Global Parameters (16)
 
   Phi1_c1  
 
   r2
Value: 100.0
Constant
 
   R1
Value: 6.0
Constant
 
   Phi_minus1_c1  
 
   k1
Value: 44.0
Constant
 
   R3
Value: 50.0
Constant
 
   Phi2_c1  
 
   k2
Value: 26.5
Constant
 
   r4
Value: 20.0
Constant
 
   Phi3_c1  
 
   k3
Value: 1.6
Constant
 
   R5
Value: 1.6
Constant
 
   Phi1_c2  
 
   Phi_minus1_c2  
 
   Phi2_c2  
 
   Phi3_c2  
 
IP3R mediated Ca release Cell1 (2)
 
   kf
Value: 28.0
Constant
 
   p
Value: 0.2778
Constant
 
ATPase pump mediated Ca efflux Cell1 (2)
 
   Vp
Value: 1.2
Constant
 
   Kp
Value: 0.18
Constant
 
IP3R independent Ca release Cell1 (1)
 
   Jleak
Value: 0.2
Constant
 
Open to Inactivated state transition Cell1 (1)
 
   p
Value: 0.2778
Constant
 
IP3R mediated Ca release Cell2 (2)
 
   kf
Value: 28.0
Constant
 
   p
Value: 0.2778
Constant
 
ATPase pump mediated Ca efflux Cell2 (2)
 
   Vp
Value: 1.2
Constant
 
   Kp
Value: 0.18
Constant
 
IP3R independent Ca release Cell2 (1)
 
   Jleak
Value: 0.2
Constant
 
Open to Inactivated state transition Cell2 (1)
 
   p
Value: 0.2778
Constant
 
Diffusion of Ca between cells (1)
 
   D
Value: 0.01
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000058

Curator's comment: (updated: 18 Dec 2006 22:50:25 GMT)

Same amplitude antiphase calcium oscillations of coupled cells as depicted in Fig 5 b of the paper. Simulation result obtained from MathSBML.

spacer
spacer