Kummer2000 - Oscillations in Calcium Signalling

  public model
Model Identifier
BIOMD0000000329
Short description
Kummer2000 - Oscillations in Calcium Signalling

Simplified (3-variable) calcium oscillation model Kummer et al. (2000) Biophys. J. 79, 1188-1195 This model is defined in a small compartment with low concentrations. You can run it first with the LSODA ODE solver and then with the Gillespie Monte Carlo method (in Time Course widget). This illustrates that at low particle numbers, as here, the stochastic simulation and the ODE approach produce different results (the stochastic approach is more correct in these circumstances). This file also demonstrates the use of several different plots to visualize results, including a histogram.

This model is described in the article:

Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G.
Biophys. J. 2000 Sep; 79(3): 1188-1195

Abstract:

We present a new model for calcium oscillations based on experiments in hepatocytes. The model considers feedback inhibition on the initial agonist receptor complex by calcium and activated phospholipase C, as well as receptor type-dependent self-enhanced behavior of the activated G(alpha) subunit. It is able to show simple periodic oscillations and periodic bursting, and it is the first model to display chaotic bursting in response to agonist stimulations. Moreover, our model offers a possible explanation for the differences in dynamic behavior observed in response to different agonists in hepatocytes.

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.

Format
SBML (L2V4)
Related Publication
  • Switching from simple to complex oscillations in calcium signaling.
  • Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G
  • Biophysical Journal , 9/ 2000 , Volume 79 , pages: 1188-1195 , PubMed ID: 10968983
  • European Media Laboratory, 69118 Heidelberg, Germany. ursula.kummer@eml.villa-bosch.de
  • We present a new model for calcium oscillations based on experiments in hepatocytes. The model considers feedback inhibition on the initial agonist receptor complex by calcium and activated phospholipase C, as well as receptor type-dependent self-enhanced behavior of the activated G(alpha) subunit. It is able to show simple periodic oscillations and periodic bursting, and it is the first model to display chaotic bursting in response to agonist stimulations. Moreover, our model offers a possible explanation for the differences in dynamic behavior observed in response to different agonists in hepatocytes.
Contributors
Vijayalakshmi Chelliah

Metadata information

is
BioModels Database MODEL1105060000
BioModels Database BIOMD0000000329
isDescribedBy
PubMed 10968983
hasTaxon
isVersionOf
occursIn
Brenda Tissue Ontology hepatocyte

Curation status
Curated

Tags
Name Description Size Actions

Model files

BIOMD0000000329_url.xml SBML L2V4 representation of Kummer2000 - Oscillations in Calcium Signalling 20.13 KB Preview | Download

Additional files

BIOMD0000000329.svg Auto-generated Reaction graph (SVG) 14.81 KB Preview | Download
BIOMD0000000329_urn.xml Auto-generated SBML file with URNs 19.96 KB Preview | Download
BIOMD0000000329.sci Auto-generated Scilab file 1.76 KB Preview | Download
BIOMD0000000329.m Auto-generated Octave file 4.61 KB Preview | Download
BIOMD0000000329.vcml Auto-generated VCML file 26.38 KB Preview | Download
BIOMD0000000329.xpp Auto-generated XPP file 2.83 KB Preview | Download
BIOMD0000000329.pdf Auto-generated PDF file 172.37 KB Preview | Download
BIOMD0000000329-biopax3.owl Auto-generated BioPAX (Level 3) 12.81 KB Preview | Download
BIOMD0000000329-biopax2.owl Auto-generated BioPAX (Level 2) 9.29 KB Preview | Download
BIOMD0000000329.png Auto-generated Reaction graph (PNG) 33.46 KB Preview | Download

  • Model originally submitted by : Vijayalakshmi Chelliah
  • Submitted: May 6, 2011 3:43:12 PM
  • Last Modified: Dec 11, 2014 4:20:22 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Dec 11, 2014 4:20:22 PM
    • Submitted by: Vijayalakshmi Chelliah
    • With comment: Current version of Kummer2000 - Oscillations in Calcium Signalling
  • Version: 1 public model Download this version
    • Submitted on: May 6, 2011 3:43:12 PM
    • Submitted by: Vijayalakshmi Chelliah
    • With comment: Original import of Kummer2000_CalciumSpiking
Legends
: Variable used inside SBML models


Species
Reactions
Reactions Rate Parameters
compartment*constant*a

compartment*constant*a
constant=2.9
compartment*V*b*a/(Km+a)

compartment*V*b*a/(Km+a)
V=1.52; Km=0.19
compartment*V*c/(Km+c)

compartment*V*c/(Km+c)
V=153.0; Km=0.16
compartment*v

compartment*v
v=0.212
compartment*V*c*a/(Km+a)

compartment*V*c*a/(Km+a)
V=4.88; Km=1.18
compartment*constant*a

compartment*constant*a
constant=1.24
compartment*V*b/(Km+b)

compartment*V*b/(Km+b)
Km=29.09; V=32.24
compartment*constant*a

compartment*constant*a
constant=13.58
Curator's comment:
(added: 11 Dec 2014, 16:14:18, updated: 11 Dec 2014, 16:14:18)
This model correspond to the core model (3 variable model defined by equations 6 to 8) of the reference publication. Figure 7 of the paper has been reproduced here. The simulation was done using Copasi v4.14 (Build 89) and the plot was generated using Gnuplot.