Search found 5752 matches

by ted
Sat Aug 20, 2005 5:51 pm
Forum: Anatomically detailed models
Topic: Reducing complex models to equivalent cables
Replies: 9
Views: 10806

Re: Code for converting to a single equivalent cable

I have been trying to modify the attshape.hoc file I hope you were working on a duplicate copy of attshape.hoc, in some directory other than where attshape.hoc is located. It's not a good idea to do anything to the installed files or directories themselves; too easy to break stuff or--much worse--i...
by ted
Tue Aug 16, 2005 1:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: two questions about channel builder
Replies: 3
Views: 4685

I learn something new every day. NEURON Main Menu / Build / Channel Builder / Import KSChan does indeed offer a list of "uncontrolled" KSChans (i.e. KSChans that are not already managed by a ChannelBuilder GUI tool. But I wonder if there are any side-effects to be concerned about. To find out, I sav...
by ted
Tue Aug 16, 2005 11:25 am
Forum: MSWin
Topic: Possible solution for: oc> Cannot allocate memory
Replies: 3
Views: 5586

Thanks. I haven't seen that error msg yet, but if it occurs I now know
what to do.
by ted
Tue Aug 16, 2005 11:24 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Stability of steady state approximation
Replies: 3
Views: 5767

Re: Stability of steady state approximation

[quote=]I'm wondering whether the steady state approximation is introducing excessive stiffness (in the form of a time constant equal to 0) into the dynamics, leading to instability of the steady state approximation?[/quote] Probably. Using your toy model "as is," reducing dt to 0.005 ms or changing...
by ted
Tue Aug 16, 2005 10:23 am
Forum: Adding new mechanisms and functions to NEURON
Topic: two questions about channel builder
Replies: 3
Views: 4685

Re: two questions about channel builder

These are good questions. - I create a channel and everything works fine with it: I can insert it into my compartment and it behaves as expected. But then, if I close the CB window, how can I edit the channel model again? If I call the CB, another session is started as if I'm creating a new channel....
by ted
Tue Aug 09, 2005 5:51 pm
Forum: Other questions
Topic: how to read from, and record data into binary files?
Replies: 7
Views: 10167

Excellent, Konstantin! Score a big point for portability of binary files.
by ted
Sat Aug 06, 2005 2:02 pm
Forum: Other questions
Topic: continue simulation until numSpikes = n
Replies: 2
Views: 3756

Using the event delivery system to terminate a simulation

It should be much more efficient to do what you want with NEURON's event delivery system. In its simplest form, the NetCon class's record() method can capture spike times to a Vector for your later use, e.g. objref nc, nil nc = new NetCon( source , nil) objref stv stv = new Vector() nc.record(stv) I...
by ted
Sat Aug 06, 2005 11:15 am
Forum: Anatomically detailed models
Topic: Reducing complex models to equivalent cables
Replies: 9
Views: 10806

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...
by ted
Tue Aug 02, 2005 9:11 pm
Forum: Getting started
Topic: Variable step size per default?
Replies: 1
Views: 3939

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 single integration st...
by ted
Tue Aug 02, 2005 9:03 pm
Forum: Getting started
Topic: Passing an objref array by reference to a function
Replies: 3
Views: 4777

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...
by ted
Tue Aug 02, 2005 8:45 pm
Forum: Other questions
Topic: how to read from, and record data into binary files?
Replies: 7
Views: 10167

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...
by ted
Tue Aug 02, 2005 8:32 pm
Forum: Other questions
Topic: periodic stimulation?
Replies: 1
Views: 4303

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...
by ted
Sun Jul 31, 2005 10:40 am
Forum: Other questions
Topic: run neuron from a java class
Replies: 4
Views: 5177

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: 9258

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: 8837

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...