www.neuron.yale.edu

It's done all the time, but there's no gold standard for how to do it; as you have noted, there are lots of approaches to desiging reduced compartmental models, e.g. Bush, P.C. and Sejnowski, T.J. Reduced compartmental models of neocortical pyramidal cells. Journal of Neuroscience Methods 46:159-166...

Very good question, Konstantin. NEURON's default integration method is implicit ("backward") Euler, which has the distinct advantage that when dt is much larger than the largest time constant in a passive system, the states of that system reach their "infinite time" values in a s...

I've always found arrays to be limiting, because no matter how many objects I think I need today, sure enough, tomorrow I need a different number. Lists are a far more flexible way to deal with multiple objects, even objects of different classes (although this simple example sticks with objects of t...

The most powerful and flexible way to deal with file i/o is to use the File class's metods, which are described here http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/classes/file.html#File Using binary formats risks generating future problems for oneself because of cross-application...

Whatever works. But the most flexible approach is to use a mechanism that takes advantage of NEURON's event delivery system. Here's the NMODL code for Ipulse1 and Ipulse2, which can deliver one or more pulses at regular intervals. Both use self-events to govern switching the current on and off. Alth...

After I extracted the gzipped tar file to /usr/local/src/nrn-5.7,
nrnjava.html and javanrn.html are in /usr/local/src/nrn-5.7/src/nrnjava

Good question. The units used for membrane current depend on whether you're dealing with a distributed (density) mechanism or a point process. For a distributed mechanism, the current is treated as if it is distributed over the surface of the cell, and the units are "current density" (curr...

Thanks for digging into this problem. Looks like a bug that needs to be fixed. In the meantime, it's trivial for any user of a real OS (UNIX, Linux, OS X) to filter out all lines that contain a particular string--awk and sed can do this nicely, e.g. sed -n '/Spine/!p' fil.dat > fixed.dat will produc...

Ugly as a box of frogs. Can't say I've ever seen the like. The data are in your hands, so you're best situated to discover what this is all about. That is, pick a branch and try to make sense out of it. Does each xyz datum signify the head of a spine? or is it the location along the dendrite where t...

I do. Uses extracellular, designed for, and works well with, single cells. Might
bog down big net simulations, if they have lots of segments. I'll send you a copy
via email; too much code to post here.

Why is the dendrite that zig-zag like if the spines are omitted? Shouldn't it be rather straight, like the "backbone" of the dendrite?! Look at it in cvapp or NEURON's Import3D tool; if you don't see zigzags, the problem is in cvapp or the Import3D tool. If so, please let me know. But if ...

I wish I had a nickel for every simple mistake I ever made.

Here's a discussion of how model geometry is handled in NEURON-- file:///home/ted/ms/neuron/nrnhelp/help/neuron/neuron/geometry.html#Geometry Reading down through the text, notice the following: In the stylized specification, the shape model used for a section is a sequence of right circular cylinde...

I think Wil Rall did a theoretical analyais on something like this ~45 years ago for a sphere or cylinder and came to the conclusion that nonisopotentialities collapsed within (much) less than a microsecond. But what if diameter were, say, 0.1 AU or so . . . Back to reality. One might imagine three ...

Short Course Announcement USING THE NEURON SIMULATION ENVIRONMENT Satellite Symposium, Society for Neuroscience Meeting 9 AM - 5 PM on Friday, Nov. 11, 2005 Speakers to include M.L. Hines and N.T. Carnevale NEURON is a powerful and convenient simulator that handles realistic models of biophysical me...