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Object arguments (doesn't matter if HOC objects or Python objects) to HOC functions are accessed using positional notation with $o instead of just $. e.g. $o1 instead of $1. A complete example, where for laziness I define the HOC function via h(): from neuron import h # declare a HOC function that j...

Mosaic Multiscale Modeling Postdoctoral Fellowship available for combining cell biology (reaction-diffusion) and electrophysiology in the NEURON simulator (neuron.yale.edu). The position involves an unusual mix of software engineering and science, depending on the candidate’s background and interest...

where I expect methods to be associated with the section objects and instead they're accessed through the hoc object (my terminology here might be wrong). Is there some guiding rule as to why this is the case? This is a legacy artifact of NEURON's transition from a HOC-based interface which did not...

For an example addressing both (1) and (2), see the load_swc function in https://github.com/ahwillia/PyNeuron-Toolbox/blob/master/PyNeuronToolbox/morphology.py You linked to a prior thread about using SWC morphologies. Remember Ted's cautions : always check the morphology to make sure it is reasonab...

To set the temperature via Python:
With important exceptions, the Python interface is essentially the same as the HOC interface, but prefaced with an "h."

Here's a patch that fixes the issue present when compiling with newer versions of cython: it changes the tuple position into a list. diff -r b8295be34ae5 share/lib/python/neuron/rxd/geometry3d/surfaces.pyx --- a/share/lib/python/neuron/rxd/geometry3d/surfaces.pyx Mon May 02 14:29:44 2016 +0200 +++ b...

Is the morphology (in particular, the diameter) the same?

Almost. In my example, parent is the index of the parent section; parent_loc is the normalized position within that section. Thus: parent_sec = sec_list[sd['parent']] # not parent_loc, grab from sec_list not sec sec.connect(parent_sec(sd['parent_loc']), sd['section_orientation']) This last line is i...

To the best of my knowledge, there is no built-in 1-line solution, but: The key functions and classes are h.parent_connection , h.section_orientation , and h.SectionRef . It's a little tricky to do this right because of the distinction between a "true parent" and a mere "parent"....

Try permanently setting the PATH environment variable for the system instead of through the command line. (See below.) In addition, make sure you are using the 32 bit NEURON to match your 32 bit Python. For completeness, I just tried the following on a machine starting from no OS, and it worked: Ins...

Open a DOS prompt (cmd) and try running: set PATH=c:\nrn\bin;%PATH% Then (in the same window), type "python" and "import neuron". Does that work? If so, you can make the change permanent by adding c:\nrn\bin to the PATH environment variable; instructions are available here and el...

You are right that cai as defined in those models is not the average calcium concentration. That is by design. cai and cao are the two calcium concentrations made available to ion channel, pump, etc mechanisms defined in NMODL via USEION. As such, they are the concentrations that the mechanism can &...

One more change should fix that, this time in share/lib/python/neuron/__init__.py : Replace the __new__ method (starts at line 168) with def __new__(cls, *args, **kwds): kwds2 = {'hocbase': cls.htype} if 'sec' in kwds: kwds2['sec'] = kwds['sec'] return hoc.HocObject.__new__(cls, *args, **kwds2) (Dep...

Sorry about that; ironically, this was caused by an attempt to improve error checking in the hocobj_call function. A fix is to add the line: PyDict_DelItemString(kwds, "hocbase"); at line 182 in src/nrnpython/nrnpy_hoc.cpp (right before the call to hocobj_call). We'll try to update the rep...

From the comment, note that: Pointers specified at the hoc level must be used to connect the extracellular mechanism's e_extracellular and i_membrane to this mechanism's ex and im, respectively. If you're not setting the pointers, then they won't point anywhere meaningful. When the model tries to us...