This simulation was used in the following article: Neymotin SA,
McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW. Neuronal
calcium wave propagation varies with changes in endoplasmic
reticulum parameters: a computer model. Neural Computation 2015 (in
press).
The code in this folder generates Fig. 2 (basic calcium wave) and
Fig. 11 (varying AMPA synapse stimulation parameters and view effects
on the calcium wave).
The simulations were tested/developed on LINUX systems, but may run on
Microsoft Windows or Mac OS.
To run the demo, you will need the NEURON simulator (available at
http://www.neuron.yale.edu) compiled with python enabled. To draw the
output you will need to have Matplotlib installed (
http://matplotlib.org/ ).
Instructions to run the model
- unzip the file
- cd ca1dDemo
- nrnivmodl (compiles the NMODL files)
The nrnivmodl command will produce an architecture-dependent folder
with a script called special. On 64 bit systems the folder is x86_64.
Note that these simulations will run with NEURON's variable time step
activated, in order to reduce the time it takes to run the simulation.
However, the simulation can still take a long time to run, depending
on your hardware setup. Therefore, the code is setup to save
simulation data to a folder called /data within the simulation
directory.
----------------------------------------------------------------------
Running and plotting the baseline calcium wave figure (Fig. 2):
# run the following code in a terminal from within the directory
containing the model files:
python
from batch import *
baseRun() # run and save a file of numpy arrays
baseDraw() # should show a plot of fig. 2 in the article
The figure shows Ca2+ wave propagation with baseline
parameters. Elevated IP3 stimulus placed at mid-dendrite (500 um on
y-axis) after 2 s past start of simulation. The plot on the left
depicts cytosolic [Ca2+] showing a wave of increased
concentration. The plot on the right of ER [Ca2+ ] shows a mirror
image wave of decreased concentration as Ca2+ is released to cytosol.
----------------------------------------------------------------------
Running and plotting Fig. 11 (electrochemical model which shows effect
of AMPA receptor stimulation on release of calcium from ER): # you
will be running 2 simulations with 2 different configuration files
(one for no AMPA receptor stimulation and one for stimulation of AMPA
receptor with 150 inputs). Both configuration files insert a set of
ion channels in the dendritic section.
# this first simulation takes less time to run (~75 seconds on a Xeon
E5/Core i7 Integrated Memory Controller processor):
python -i cawave.py AMPA0.cfg
# the following simulation took ~54 minutes when run using the same processor:
python -i cawave.py AMPA150.cfg
To plot the output from these simulations, run the following (after
you exit from the previous simulations):
python
from batch import *
execfile('plot_fig11.py')
The figure shows electrical stimulation with increased number of AMPA
activations enhancing Ca2+ waves induced by IP3 (2.5 mM at 7 s). The
left column shows control simulation: Ca2+ wave with no AMPA inputs
prior to the IP3 stimulus. Middle column shows Ca2+ wave with train of
150 AMPA inputs (onset: 3 s; interspike interval: 25 ms) prior to the
IP3 stimulus. The column on the right is a comparison of voltage
(top), ER Ca2+ (middle), and cytosolic Ca2+ (bottom) in control
(black) and simulation with 150 AMPA inputs (red).
NOTE: If you are interested in running the simulation for a shorter
period of time, you can modify the configuration files AMPA0.cfg and
AMPA150.cfg. Change the value of tstop under [run] to the time you're
interested in (in milliseconds). However, the resulting figure will
not be identical to Fig. 11 in the publication.
----------------------------------------------------------------------
For questions/comments email:
mohamed dot sherif dot md at gmail dot com
or
samn at neurosim dot downstate dot edu
or
robert dot mcdougal at yale dot edu
Changelog
---------
20160915 This updated version from the Lytton lab allows their models
which contain misc.mod and misc.h to compile on the mac.
20220523 Updated MOD files to contain valid C++ and be compatible with
the upcoming versions 8.2 and 9.0 of NEURON.
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