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:
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.
This model is hosted on BioModels Database and identified by: BIOMD0000000329.
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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.
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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.
Submitter of this revision: Vijayalakshmi Chelliah
Modellers: Vijayalakshmi Chelliah
Metadata information
isDescribedBy (1 statement)
hasTaxon (1 statement)
isVersionOf (1 statement)
occursIn (1 statement)
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000329_url.xml | SBML L2V4 representation of Kummer2000 - Oscillations in Calcium Signalling | 20.13 KB | Preview | Download |
Additional files |
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| BIOMD0000000329-biopax2.owl | Auto-generated BioPAX (Level 2) | 9.29 KB | Preview | Download |
| BIOMD0000000329-biopax3.owl | Auto-generated BioPAX (Level 3) | 12.81 KB | Preview | Download |
| BIOMD0000000329.m | Auto-generated Octave file | 4.61 KB | Preview | Download |
| BIOMD0000000329.pdf | Auto-generated PDF file | 172.37 KB | Preview | Download |
| BIOMD0000000329.png | Auto-generated Reaction graph (PNG) | 33.46 KB | Preview | Download |
| BIOMD0000000329.sci | Auto-generated Scilab file | 1.76 KB | Preview | Download |
| BIOMD0000000329.svg | Auto-generated Reaction graph (SVG) | 14.81 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_urn.xml | Auto-generated SBML file with URNs | 19.96 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
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Version: 2
- Submitted on: Dec 11, 2014 4:20:22 PM
- Submitted by: Vijayalakshmi Chelliah
- With comment: Current version of Kummer2000 - Oscillations in Calcium Signalling
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Version: 1
- Submitted on: May 6, 2011 3:43:12 PM
- Submitted by: Vijayalakshmi Chelliah
- With comment: Original import of Kummer2000_CalciumSpiking
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revisions as only public revisions are displayed here. Any private revisions
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: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| a Guanine nucleotide-binding protein subunit alpha-11 |
0.01 nmol |
| b 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 |
0.01 nmol |
| c calcium(2+) |
0.01 nmol |
| Reactions | Rate | Parameters |
|---|---|---|
| a => ; b | compartment*V*b*a/(Km+a) | V=1.52; Km=0.19 |
| => b; a | compartment*constant*a | constant=1.24 |
| => a; a | compartment*constant*a | constant=2.9 |
| c => | compartment*V*c/(Km+c) | V=153.0; Km=0.16 |
| => a | compartment*v | v=0.212 |
| => c; a | compartment*constant*a | constant=13.58 |
| b => | compartment*V*b/(Km+b) | Km=29.09; V=32.24 |
| a => ; c | compartment*V*c*a/(Km+a) | V=4.88; Km=1.18 |
(added: 11 Dec 2014, 16:14:18, updated: 11 Dec 2014, 16:14:18)