This is the readme for the Stochastic calcium spikes models published in:

Anwar H, Hepburn I, Nedelescu H, Chen W, De Schutter E (2013)
Stochastic calcium mechanisms cause dendritic calcium spike
variability. J Neurosci (in press)

Scripts Authors: 

Haroon Anwar: haroon.anwar@gmail.com
Iain Hepburn: ihepburn@oist.jp

The scripts are available through this link:
http://senselab.med.yale.edu/modeldb/data/AnwarEtAl2013.zip

Software Requirements:

These scripts run on STEPS 2.x, which can be found at
http://steps.sourceforge.net.

List of Meshes:

	* 5 cylindrical meshes of lengths 10 um, 20 um, 40 um, 80 um
                 and 160 um can be found in folder named
                 'meshes'. These cylindrical meshes can be used with
                 scripts 1-9.
	* A dendritic mesh ('chop_mesh.inp') can also be found in
                 folder named "meshes". This mesh can be used with
                 scripts 10 and 11.

List of Scripts:

	1. The script 'StochasticCaburst.py' was used with all
	cylindrical meshes mentioned above to simulate calcium bursts
	shown in Figure 2A-C. The traces generated using this script
	were used for analysis shown in Figure 2 E, Figure 4 and
	Figure 8D-F.
	2. The script 'StochasticHH.py' was used with all cylindrical
	meshes mentioned above to simulate HH spikes shown in Figure
	2D. The traces generated using this script were used for
	analysis shown in Figure 2F, Figure 3.
	3. The script 'HybridCaburst_stochCaP.py' was used cylindrical
	mesh of 10 um length to simulate calcium bursts shown in
	Figure 5A.
	4. The script 'HybridCaburst_stochCaT.py' was used cylindrical
	mesh of 10 um length to simulate calcium bursts shown in
	Figure 5B.
	5. The script 'HybridCaburst_stochBK.py' was used cylindrical
	mesh of 10 um length to simulate calcium bursts shown in
	Figure 5C.
	6. The script 'HybridCaburst_stochSK.py' was used with
	cylindrical mesh of 10 um length to simulate calcium bursts
	shown in Figure 5D.
	7. The script 'StochasticCaburst_cluster.py' was used with
	cylindrical mesh of 40 um length and variable number of CaP
	channels clustered with BK channels to simulate calcium bursts
	shown in Figure 6.
	8. The script 'HybridCaburst_detchannels.py' was used with all
	cylindrical meshes mentioned above to simulate calcium bursts
	and their analysis shown in Figure 7.
	9. The script 'StochasticCaburst_wellmixed.py' was used with
	all cylindrical meshes described above to simulate stochastic
	calcium bursts shown in Figure 8A-C. The races generated using
	this script were used for analysis in Figure 8D-F
	10. The script 'StochasticCaburst_dendrite.py' was used with
	dendritic mesh ('chop_mesh.inp') to simulate synaptically
	evoked dendritic calcium bursts shown in Figure 10C and Figure
	11.
	11. The script 'StochasticCaburst_dendrite_ampa.py' was used
	with dendritic mesh ('chop_mesh.inp') to simulate dendritic
	calcium bursts shown in Figure 10D and Figure 12.