Search found 5785 matches

by ted
Sun Jul 31, 2005 10:40 am
Forum: Other questions
Topic: run neuron from a java class
Replies: 4
Views: 5223

Location of nrnjava.html and javanrn.html

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
by ted
Sat Jul 30, 2005 6:26 pm
Forum: Anatomically detailed models
Topic: Area Calculation - Channel Density
Replies: 6
Views: 9384

Units, density (distributed) mechanisms, and point processes

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" (current/area, ...
by ted
Thu Jul 28, 2005 10:16 am
Forum: Anatomically detailed models
Topic: import of neurolucida .asc
Replies: 6
Views: 8949

Using sed to eliminate troublesome lines from a file

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...
by ted
Wed Jul 27, 2005 8:11 pm
Forum: Anatomically detailed models
Topic: import of neurolucida .asc
Replies: 6
Views: 8949

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...
by ted
Wed Jul 27, 2005 3:05 pm
Forum: Modeling networks
Topic: extracellular field generation
Replies: 4
Views: 7477

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.
by ted
Wed Jul 27, 2005 2:55 pm
Forum: Anatomically detailed models
Topic: import of neurolucida .asc
Replies: 6
Views: 8949

Re: import of neurolucida .asc

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 you do see...
by ted
Wed Jul 27, 2005 12:37 pm
Forum: Anatomically detailed models
Topic: area calculation?
Replies: 3
Views: 6769

I wish I had a nickel for every simple mistake I ever made.
by ted
Tue Jul 26, 2005 1:07 pm
Forum: Anatomically detailed models
Topic: area calculation?
Replies: 3
Views: 6769

Geometry

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...
by ted
Tue Jul 26, 2005 11:38 am
Forum: Anatomically detailed models
Topic: Modelling spherical cell
Replies: 1
Views: 4543

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 ...
by ted
Mon Jul 25, 2005 1:36 pm
Forum: NEURON Announcements
Topic: NEURON course at SFN 2005 Meeting
Replies: 0
Views: 13061

NEURON course at SFN 2005 Meeting

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...
by ted
Sun Jul 24, 2005 12:15 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Stability of steady state approximation
Replies: 3
Views: 5847

Re: Stability of steady state approximation

The problem almost certainly arises in the expression for minf, which contains subexpressions that become indeterminate when v == 35 (as does the expression for malpha). Try rewriting these using L'Hospital's rule and see if that doesn't fix the problem. Since lim x / (exp(k*x) - 1) as x -> 0 is 1/(...
by ted
Thu Jul 21, 2005 10:33 am
Forum: MSWin
Topic: cygwin bugs
Replies: 0
Views: 4140

cygwin bugs

The MSWin distribution of NEURON uses cygwin for its terminal ("interpreter window") and some other purposes. cygwin is very much a live project, and each release of it comes with its own bugs, which may affect NEURON. Some examples of this are described here https://www.neuron.yale.edu/phpBB2/viewt...
by ted
Fri Jul 15, 2005 5:30 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: psth and calculating firing rates
Replies: 2
Views: 7090

Re: psth and calculating firing rates

Michael Hines, or probably Bill Lytton, can tell you where the source code for the Vector class's methods is located. In order to take advantage of psth, you will first have to bin your spike times. You can do binning as postprocessing i.e. after the end of a simulation run, so its implementation ca...
by ted
Fri Jul 15, 2005 4:57 pm
Forum: Anatomically detailed models
Topic: failure to "update" diam
Replies: 1
Views: 3930

Computation of effective L and diam is deferred

NEURON keeps 3D data in internal data structures that respond immediately in response to the various pt3d . . . statements. However, determining effective diameters, areas etc. requires actual computation, so for the sake of efficiency is deferred until a func or proc is called that really needs suc...
by ted
Thu Jul 14, 2005 1:01 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using a variable value from a mechanism
Replies: 2
Views: 4191

Use POINTER. For specific examples of the use of POINTER, see the gap junction and continuous transmitter release models in chapter 10 of The NEURON Book http://www.neuron.yale.edu/ftp/ted/book/revisions/chap10indexedref.pdf I see that the documentation of PARAMETER has been slightly mangled in the ...