www.neuron.yale.edu

Here is how I build on a OS X G5 NSRC=$HOME/neuron/nrn IVSRC=$HOME/neuron/ivcarbon NOBJ=$HOME/neuron/nrncarbon IDIR=/Applications/NEURON-5.8 put the nrn*tar.gz sources in NSRC and the iv*tar.gz sources in IVSRC cd $IVSRC ./configure --prefix=$IDIR/iv --enable-carbon make make install cd $NOBJ $NSRC/...

For mswin, use a "-fn 20" argument pair when launching the rxvt terminal.
For nrngui you do this in the
c:/nrn58/lib/neuron.sh script.

With regard to question 3, I would encourage you to compare the results and performance of the fixed step method with decreasing dt and secondorder=0 and secondorder=2 and the results of the variable step method with decreasing atol. I am guessing you will be very pleased with the variable step meth...

The intention is that Python be a native alternative to HOC. I've gotten quite far now on the section and segment interface and most of the idioms I've learned just get repeated now over and over. As soon as the mod file interface has become automatic I'll start asking for help on the tedious proces...

See http://www.neuron.yale.edu/neuron/stati ... html#xmenu
You are interested in the xpanel("menubar") ... xpanel()
fragment

It might not be too difficult to modify the nrnivmodl and nrniv_makefile scripts in nrn/bin (actually the *.in precursor files if you have autoconf/automake/libtool installed) to look at the suffixes of the files you pass to nrnivmodl (default is all the mod files in the working directory). Then you...

I'd like to hear people's comments about the following. The hierarchy is section, segment, mechanism, rangevariable. [hines@NeuronDev nrnpy]$ cat demo.py from section import * soma = Section() print soma soma.insert(hh) for seg in soma : print seg for m in seg : print m for rv in m : print rv soma.n...

That syntax is attractive in its clarity. But I don't immediately see how s.hh.gnabar = .12 when s.nseg = 50 ends up setting the gnabar value in all 50 segments. I think andrew's idea (pace someone who actually knows python) is that would be done with s[].hh.gnabar = .12 Can a python person tell me ...

in your working directory containing the nrnmech.dll file remove all the *.c, *.o, and nrnmech.dll files and rerun mknrndll. If that does not work, did the sim work on your old machine? What is the NEURON version? Can you launch the NEURONDEMO? Did you happen to separately install a full version of ...

...I wonder what is the impact of this on the calculation speed... The question may be moot since nmodl is not capable (without VERBATIM block c programming) of defining single channel models. However, from the perspective of deterministic channels, KSChan should be slightly (though probably not me...

That's right. Since you have a ligand sensitive transition, the internal data structure is updated every time step. Since you are still having problems, you should send me (michael.hines@yale.edu) the hoc/ses/mod files in a zip file that are needed to run the model.

You can change the vector values at any time, even every time step, during a run. However, in the single channel (Nsingle > 0) case there is an internal data structure based on the rate values that you will need to tickle to get it updated if any of the rate vector values change. These normally get ...

Hi Andrew, That is strange. I did not get notified by email that a post was added to that topic and the forum claims I am watching it. I wonder if my spam filter is inadvertently throwing away those notifications. Anyway, I am delighted for you to be involved. I am still working on the parallel comp...

It is the area of the compartment (segment) to which the node of the electrical device (resistor or capacitor) connects. Only equations (matrix rows) that add to the current balance equations need units consistent with the current balance equations. Matrix rows not associated with segments can have ...

Before typing "nrngui" check your DISPLAY environment variable with echo $DISPLAY and see what it says. If there is no DISPLAY then you need to set it. If there is, then does it still work with the --nogui option? If you have been using the CVS archive for some time then the most recent ch...