IP3R model comparison (Hituri and Linne 2013)

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Accession:147367
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.
Reference:
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):
Channel(s):
Gap Junctions:
Receptor(s): IP3;
Gene(s):
Transmitter(s):
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;
/
IP3R_models
models
README.txt
run_IP3R_P0.m
                            
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
http://steps.sourceforge.net/STEPS

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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