IP3R model comparison (Hituri and Linne 2013)

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In this study, four models of IP3R (Othmer and Tang, 1993; Dawson et al., 2003; Fraiman and Dawson, 2004; Doi et al., 2005) were selected among many to examine their behavior and compare them with experimental data available in literature. The provided MATLAB script (run_IP3R_P0.m) will run the simulations and plot Figure 2A in the paper.
1 . Hituri K, Linne ML (2013) Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations. PLoS One 8:e59618 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Channel/Receptor;
Brain Region(s)/Organism: Unknown;
Cell Type(s):
Gap Junctions:
Receptor(s): IP3;
Simulation Environment: STEPS;
Model Concept(s): Ion Channel Kinetics; Calcium waves;
Implementer(s): Hituri, Katri [katri.hituri at gmail.com];
Search NeuronDB for information about:  IP3;
Hituri K, Linne M-L (2013) Comparison of Models for IP3 Receptor
Kinetics Using Stochastic Simulations. PLoS ONE 8(4):
e59618. doi:10.1371/journal.pone.0059618

We provide scripts for the four models compared in our study:

Othmer HG, Tang Y. Oscillations and waves in a model of
InsP3-controlled calcium dynamics, London: Plenum Press, volume 259 of
Experimental and Theoretical Advances in Biological Pattern
Formation. pp. 277-300, 1993

- Dawson A, Lea E, Irvine R. Kinetic model of the inositol
  trisphosphate receptor that shows both steady-state and quantal
  patterns of Ca2+ release from intracellular stores. Biochem J
  370:621, 2003

- Fraiman D, Dawson SP (2004) A model of IP3 receptor with a luminal
calcium binding site: stochastic simulations and analysis. Cell
Calcium 35: 403-413, 2004

- Doi T, Kuroda S, Michikawa T, Kawato M (2005) Inositol
1,4,5-trisphosphate-dependent Ca2+ threshold dynamics detect spike
timing in cerebellar Purkinje cells. J Neurosci 25: 950-961, 2005

The work described in the study was done with STEPS version 1.1.2. on
a Linux computer and has not been tested on newer versions.
For more information about STEPS, please visit

The scripts require that you also have NumPy installed.  For more
information about NumPy, please visit http://www.numpy.org/

The Figures in our publication were plotted with MATLAB. The provided
MATLAB script (run_IP3R_P0.m) will run the simulations and plot the
Figure 2A in the our publication. The simulations will take several
hours. Simulation results are stored in ip3r_MODELNAME_op_res.dat
files and used Ca2+ concetrations in ip3r_MODELNAME_op_ca_concs.dat
files. Please read run_IP3R_P0.m for more information about running
the simulations and plotting the results.

If you do not have MATLAB available you can run the simulations from
command line:
- go to the folder IP3Rmodels

- run each of the simulations separately (each will take time from 10
  min to 2 h):
	python models/sim_doi.py
	python models/sim_fd.py
	python models/sim_dli.py
	python models/sim_ot.py
- the results will be stored in .dat files and you can use a software
  of your choise to plot them

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