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<html><pre>
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: [email protected]
Iain Hepburn: [email protected]
The scripts are available through this link:
<a href="http://senselab.med.yale.edu/modeldb/data/AnwarEtAl2013.zip">http://senselab.med.yale.edu/modeldb/data/AnwarEtAl2013.zip</a>
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.
</pre></html>