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 20160915 This updated version from the Lytton lab allows their models which contain misc.mod and misc.h to compile on the mac.