www.neuron.yale.edu

Hi, from the online documentation of forall ( http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/secspec.html#forall ): Within an object, forall refers to all the sections declared in the object. This is generally the right thing to do when a template creates sections but is inconvenie...

Hi, I found that there was a change in how one has to set the equilibrium potential from Python that introduced some bugs in my simulations. In versions 6.2 and 7 up to svn rev. 2227, I could set the equilibrium potential as follows: from neuron import h s = h.Section() s.insert("hh") for ...

Here is a debian package of the latest hg revision:
http://www.stimfit.org/nrn-7.0-223_Ubun ... d.i386.deb
It's not alienated and I haven't extensively tested it, so please report bugs.
Christoph

I don't have any experience with 64 bit systems. However, my guess would be that the 64-bit version of the ncurses library is missing on your system. Maybe or will help?

Could you give some more details, e.g. which nrnzip file exactly did you use, and what was the error message? On my system, mos2nrn works when installed from an "alienated" rpm. From the command line, I can do: $ /usr/local/nrn/i686/bin/mos2nrn file.nrnzip which will pop up a new shell, co...

I had to include stdlib.h in src/nrncvode/netcvode.cpp in addition to the files mentioned above on my system (gcc 4.3.2). Here is the patch against hg changeset 210: diff -r 482ea9727cc4 src/ivoc/ivocrand.cpp --- a/src/ivoc/ivocrand.cpp Mon Oct 20 14:36:51 2008 -0400 +++ b/src/ivoc/ivocrand.cpp Wed ...

Hi, I have created a debian package for Ubuntu (Hardy, 8.04.1) by converting the rpm with alien. I've tested it on a naive system (i.e. NEURON wasn't previously installed) which worked without any obvious problems. I would be happy to share the Debian package if anyone has some 4.2 MB of web space t...

From hoc, you could do: objref ic, g g = new Graph() ic = new IClamp1(0.5) g.addvar("ic.i") addplot(g, 0) Alternatively, you can use the GUI: Choose "Graph->Current axis" from the menu, right-click on the graph, select "Plot what", left-click "Show->All" in th...

I just saw the changes to the "for seg in sec" and "for seg in sec.allseg()" syntax in http://www.neuron.yale.edu/cgi-bin/trac ... geset/2195. That fixes the problem, thank you very much!
Christoph

The following code worked fine for me: #! /usr/bin/python from neuron import h import numpy h("""load_file("stdrun.hoc")""") h.tstop = 10; h.dt = 0.01; h.steps_per_ms = 1.0/h.dt soma = h.Section() estim = h.SEClamp( soma(0.5) ) g_exc = numpy.arange( 10, 10+h.t...

There is a slight inconsistency regarding how mechanisms in terminal nodes are handled from hoc and Python. Consider the following hoc code: create s s { nseg = 1 insert pas for (x) print x, g_pas(x) } This will print: 0 0.001 0.5 0.001 1 0.001 Obviously, calling g_pas(0) or g_pas(1) will return its...

I have not found any reference to it in the NMODL documentation, and the forum search only results in examples of it, with question unrelated to the command itself. What does it do? It's basically a look-up table that may help to speed up simulations: http://www.neuron.yale.edu/neuron/static/docs/h...

And yes my data file has same time values in many rows ! I'm a bit puzzled: Did you use the code that I've posted above, but you still have the same time values in subsequent rows? That would be strange. Can one set the accuracy of the data in NEURON like one can do in C++ ? If you refer to the pur...

matvol.fprint(filvol) I have to admit that I had great problems making the File class produce formatted output using format specifiers such as "%.4f" or similar on my system. It always resulted in some truncation errors. The same may have happened to you, which might explain why there wer...

How can I improve the voltage resolution of my simulations. Using a step size of 25 usec I often get same voltage values for a period of 250usec at a stretch. I want resolution on the scale of 25usec. Could you provide a minimal, stand-alone hoc sample that will reproduce the behaviour that you des...