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If you're using NEURON 7.3 or higher, neuron.nrn_dll() returns a ctypes object corresponding to the NEURON library. The main difficulty here is that the C API exists only informally; there is no documentation or promise of what functions will have a stable interface, but you are encouraged to poke a...

There is a subtle and unfortunate distinction between h.run and neuron.run. The full code of neuron.run (defined here ) is: def run(tstop): """ function run(tstop) Run the simulation (advance the solver) until tstop [ms] """ h('tstop = %g' % tstop) h('while (t < tstop) ...

The safest way to avoid any risk of cross-contamination from multiple experiments is to run them independently in separate processes. Obviously, doing this manually is not a good use of your time. You could write a shell script that launches NEURON repeatedly with arguments indicating what simulatio...

As long as a species has a "name" and lives on an rxd.Region with nrn_region = 'i' (or 'o'), then its concentrations will respond to currents. You have a minor syntactic error: rxd.Region takes a list of sections; it does not accept a string. For example, you could do something like: from ...

As of 7.4 (978), Python threads do not execute when the HOC interpreter is waiting for input. To do interactive matplotlib and interviews graphics simultaneously from HOC, simply run a two-line python wrapper. For example, test.hoc, below plots y = x ^ 2 in both Interviews and matplotlib windows: nr...

I was asked to share my thoughts. The grant guidelines are long, so here's a little more context: "There is no prescribed single license... however... reviewers will be instructed to evaluate dissemination plans relative to these goals," which includes providing a license that "permit...

This is an issue for me since every time I run my program in the same python interpreter, the hoc interpreter is not cleared and new sections are added to the previous ones. The workaround that always works is to create a class based on your model cell. An alternative strategy for non-interactive p...

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?