www.neuron.yale.edu

Is there any way to record only during a period of time much shorter than t stop I mean something like if(t>=tstart &&t<=tstp){vec.record(..)...} ? No. I think there is, actually. First, create an FInitializeHandler instance FInitializeHandler(1, init) next, write the "init" routi...

That is a large block. Do you know where and why it is being requested? Yes, it occurs while "loading" NEURON's event queue, i.e. within the following set of nested loops: for i in range(numCells): for j in range(numExCells): if exNetConArray[i,j] != None: for (k,spikeTime) in enumerate(e...

1) I installed version 7.1 (much easier than I expected: thanks for the precompiled binaries), and I get the same behavior. 2) I only *think* the requested block size is 1048580096, based on the error message (quoted above) which I may be misunderstanding. 3) I, too, thought of the "two fold si...

Thanks, will do.
I thought updating to 7.1 might be the thing to do, but when I searched the Hg repository for "leak," I didn't find anything newer than 7.0.

My model seems to be leaking memory. I've had no success, so far, debugging it myself. Results so far seem to implicate NEURON, rather than Python, but I'm not 100% confident of that. Unless I'm very lucky, nobody's going to be able to tell me the solution, but I'd like suggestions about how to proc...

I am trying to do something complicated with the event delivery system, and clearly not doing it right: I'd like to know what I'm doing wrong. The full error message is: /Applications/NEURON-7.0/nrn/umac/bin/nrniv: GABAa_S[599] :Event arrived out of order. Must call ParallelContext.set_maxstep AFTER...

My questions, from specific to general, are: Is there a way to call a Python method from inside a Hoc proc? If I modify advance() as described below, will I slow down execution horribly? Is there some other better, or more conventional way than the one described below to accumulate output on disk, r...

Alright, I've replicated the problem with a toy program. It boils down to an instance of unexpected behavior at the interface between NEURON and NMODL when combining NET_RECEIVE{INITIAL{}} with Netcon.event() The elements are as follows: One cell template simpleCell 2 presynaptic cells, instances of...

In a synaptic mechanism I wrote in NMODL, I attempted to read the value of the connecting Netcon.weight at intialization time. Specifically, my NET_RECEIVE block contained this line: gmax = weight which executed *before* the first Netcon event occurred. This didn't work. If I understand correctly, t...

when you built with 2.5.1, that the python library that got linked was a 2.3 or 2.4? Right, that's probably the explanation. Sorry. I've got multiple copies of various versions of Python in various places, and have had problems before with NEURON finding the wrong one -- in particular 2.4 when I wa...

I checked out & built revision 2195, and, when I ran neuron with the -python switch, got this warning: sys:1: RuntimeWarning: Python C API version mismatch for module nrn: This Python has API version 1012, module nrn has version 1013. I was using Python 2.5.1 I installed Python 2.5.2 and the war...

Hang on a minute: I just noticed there's apparently a trac ticket for this. Is this the issue that was fixed in revision 2192?
If so, do I need to get the source from the SVN repository, or is it enough to download the latest precompiled installer for the current standard distribution?

I'm debugging the Python-port of a model originally coded in hoc. Of course, I'm aiming to get the Python version to generate the same output as the hoc version. There's still a subtle difference, which I've tracked down to a particular synapse. I need a way to look more closely at that synapse, to ...

Some Mac users prefer BBEdit. It costs about $200. I wouldn't bother with it; has too many extraneous features and is far too expensive. I use BBedit, and like it a lot, but I concede that a really high-powered text editor is only useful if you do a lot of programming, and I definitely conceed that...

Sometimes, in NEURON one needs a NULLObject, for example, when creating a NetCon with a source, but no target, or vice versa. (In the following toy example, I create a NetCon with no source *and* no target, which is legal, 'though useless.) oc>objref nil,nc oc>nc = new NetCon(nil,nil) oc>nc.event(5)...