www.neuron.yale.edu

Pure Python version, thanks to mctavish:

Is there a way to work with strdefs in the abstract in python without them being evaluated to a particular value? For example, the List object's browser method takes a strdef and a function that is called repeatedly which is supposed to change the strdef to define list labels. In the following code,...

According to The NEURON Book page 109, arc3d(i) is the anatomical distance of the ith 3-D point from the 0 end of the section. I think the following code constructs two sections s1 and s2, makes s2 a child of s1 whose 1 end is connected to s1's 1 end, and then prints their x, y, z, and arc length va...

I tried building interviews from scratch on a mostly standard Ubuntu system. I had to install libx11-dev, but otherwise I basically just cloned the hg repository, ran build.sh, configure, then make. Make fails at the step: /bin/bash ../../../libtool --mode=link g++ -g -O2 -o idraw idarrow.o idarrowh...

RangeVarPlots will respect Keep Lines if you add them to the flush_list and display them using h.flushPlot() (but not w.flush()). My final working code is w=h.Graph() # create graph window w.size(-totalLength*.05, totalLength, -.0001, .002) # set axes stick.push() cai_rvp=h.RangeVarPlot('cai') cai_r...

I do not want smooth updates of RangeVarPlots. I want to see (effectively) RangeVarPlots for different time values overlapping each other, as in the first two code examples. The problem is that RangeVarPlot seems to ignore the keeplines property; even if you call .family(1), the previous lines disap...

I want to plot the concentrations cai and ip3i versus position every plotEvery milliseconds, all on the same graph. I have some code that works, but it draws the lines manually and is not particularly elegant: w=h.Graph() w.size(0, totalLength, 0, 2) w.color(1) w.label('cai') w.color(2) w.label('ip3...

Thanks for clarifying about the K.

Can I safely include mod files without SOLVE statements without affecting the stability of the rest of the system?

I was looking at the same file earlier today. It seems like I can do without using any solve statements or state variables, as in: NEURON { SUFFIX nap USEION na READ ena WRITE ina RANGE gnabar,vhalf, K } UNITS { (mA) = (milliamp) (mV) = (millivolt) } PARAMETER { : parameters that can be entered when...

I recently discovered from http://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=489 that cvode should work with kinetic models (but does it work with LONGITUDINAL_DIFFUSION?) My first couple attempts ended in mysterious "bus error(s)," so I decided to start over from the beginning, an...

I have a partial solution to my own question. I can open a shape plot and resize, etc... it entirely* in python by # ready shape plot h.newshapeplot() shapeWindow=h.fast_flush_list.object(h.fast_flush_list.count()-1) shapeWindow.size(-380.24,488.164,-624.858,170.347) shapeWindow.variable('cai') shap...

I have recently decided to learn the Python interface for Neuron. I decided the best way to learn would be to convert some of my old scripts from hoc to python. I came so close to being successful on my own, but I haven't been able to figure out how to control shape plots without invoking the hoc in...

Works great. Thanks.

Sorry to resurrect an old conversation, but... Did anyone ever figure out a good way to get the gui from python? If I start with "nrngui -python" and get a python interpretor that way, everything works wonderfully, but what I want to do is: $ python Python 2.5.2 (r252:60911, Oct 5 2008, 19...

Hines tells me "Multisplit does not work with LONGITUDINAL_DIFFUSION."