www.neuron.yale.edu

I dug up some old and very ugly code that was originally developed for a different purpose, and hacked at it until it could do the job. The result was a program that works but is far too complicated and ugly--just reading the code reminds me of the old saying that BASIC should be banned because lear...

Think like an experimentalist. Come up with a list of testable hypotheses, and test them. To help you get started, here are the hypotheses that I would test if I were you. 1. The implemenation of the gap junction is incorrect. 2. The implementation of one axon, or both axons, is incorrect. 3. The ga...

For me, it took many readings and interpretations (and the test code) to discover that there are two methods, the distance()/distance(x) pair being an older, slightly less powerful way, and the more powerful distance(0,x)/distance(1,x) There really aren't two methods. There is just a single distanc...

I'm not sure what the source of confusion is. The Programmer's Reference entry for distance() is SYNTAX distance() or distance(0, x) len = distance(x) or len = distance(1, x) DESCRIPTION Compute the path distance between two points on a neuron. distance() with no arguments specifies the origin as lo...

Not swc. It's a format generated by a "home brew" reconstruction rig developed originally by David Amaral and used subsequently by others including Brenda Claiborne. In fact, this is probably one of her cells. I have an old program that read files that contained, among other things, this k...

You might find something useful among the links on Jim Perlewitz's site--
http://home.earthlink.net/~perlewitz/

If you do find some good stuff there or elsewhere, could you please do us all a big favor
and reply to this discussion thread?

--Ted

Well, when I say "mark a section as 'priveledged'", I mean that I make a SectionRef to it and explicitly refer to it with the sectionname statement method whenever I want to use it. I didn't mean to imply that I was somehow able to use a SectionRef instance in exactly the same way as an &...

access is provided as a convenience so that there can be a default section. This should be a "conceptually priveleged" section, i.e. some part of the model whose variables and/or parameters are of particular importance to you, so you can refer to them by just using the name of the variable...

Export the channel specification to a hoc file ChannelBuilder / Properties / Clone channel type / Hoc file for KSChan Then modify the hoc file as needed to assert temerature dependent rate constants. Refer to the Programmer's Reference entries on KSChan as necessary for details. Example based on tut...

Don't use NMODL. In NEURON, stochastic channel gating mechanisms are implemented with the KSChan class, which you can read about here http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/kschan.html You will note that singhh.hoc starts with load_file("singhhchan.hoc") T...

Nothing built in to do this. You'd have to capture a series of vectors, then plot them
with incrementing vertical (and possibly horizontal) offset. Some of Alain Destexhe's
papers show graphs that were done this way.

--Ted

Discovering the mapping between section names and branches in a shape plot really involves two tasks: A. Given a branch in a shape plot, can you figure out the name of the corresponding section? B. Given the name of a section, can you figure out the corresponding branch in a shape plot? At present N...

Have you read the pdf preprint for this paper
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997
? Especially the part about range and range variables.

--Ted

I tried the code under MSWin using 5.8.88 and 5.8.113 and got this msg with both: nrniv: sAmpa :not right number of subscripts in C:/home/myhoc/horstmann/urtest2.hoc near line 36 setpointer synSignal.pre, synSignalStim.sAmpa(0.5) ^ But under Linux using version 5.8 2005-8-29 8:58:55 Main (66) it wor...

1- i read toturial to use space plot i did every thing that they said, but i see just 2 curves and nothings more, what should i do if i like to have for example 10-20 curve ? There are lots of tutorials. Which one do you mean? 2-is it possible to write a code in "hoc" to save v(x,t) to a ...