www.neuron.yale.edu

The reaction-diffusion module can be used in HOC almost identically to how it is used in Python if you begin your HOC code with: objref pyobj, h, rxd { // load reaction-diffusion support and get convenient handles nrnpython("from neuron import h, rxd") pyobj = new PythonObject() rxd = pyobj.rxd h = ...

Thanks for bringing this to our attention.

MathJax disabled their old CDN which the Sphinx plugin used, but there's now a replacement. I'll try to switch in the next few days.

See: http://docs.mathjax.org/en/latest/start.html

Are you able to import neuron from the regular Python prompt?

If so, consider that as a work-around; i.e. launch your simulation through python instead of through NEURON. If not, that can be fixed by adjusting your PYTHONPATH and maybe NEURONHOME environment variables.

At (90 s) * (1000 ms/s) * (10 timesteps/ms) * (2 values/timestep/cell) * (1500 cells) * (8 bytes/value), you're looking at 21.6 Gigabytes of data. If you're not preallocating with Vector.buffer_size, the story gets worse, since every time the vector fills up, it creates a new one (twice the size of ...

What operating system?

I just tried it on my Windows machine through Spyder, and it worked for me.

Could you try installing the latest alpha version (http://www.neuron.yale.edu/ftp/neuron/versions/alpha/) and seeing if that solves the problem?

Most immediately, the problem is that in Python libnrnmech.so is failing to load, and without that the mod file mechanisms -- in particular StdwaSA -- are unavailable. Had it loaded successfully, you wouldn't have gotten the error "dlopen failed"; instead, you would have seen the same "additional me...

The last point is quite dificalt to realize, specificaly in reconstructed morphology with many compartments. It would be very useful if I could reach segments inside a section, like this soma = h.Segment() soma.nseg = 3 soma[0].cm = 0.1 soma[1].cm = 0.2 soma[2].cm = 0.3 Same for point process: dend...

Unfortunately, your code will create 30 synapses with tiny step, which will be attached to just 3 compartments. Computational overhead will be 30/3 = 10! The add_syn function only creates at most one synapse per segment... so if nseg=3, then it creates at most three synapses. The trick is that it a...

There's nothing wrong with having multiple AMPA channels on the same segment. It's generally best to keep issues of numerics (e.g. discretization into segments) separate from the description of your model (e.g. what synapses are where). That way, you can change the mesh (e.g. increasing nseg to get ...

Actually, the error is not related directly to the sec=celllist .soma; that was correct. The convention in the NEURON documentation (and many others) is that [ and ] in the syntax specification is used to indicate optional parameters... i.e. the stuff inside the brackets can be included or not. In y...

NEURON's directory information is technically incomplete here, but please don't use section.diam as it is potentially confusing: diam is naturally a property of a segment not of a section, so reading section.diam will return the middle diameter and writing it will set all segments: >>> dend = h.Sect...

In the Python version, your current clamp does not do what you think it does. You write: istim = h.IClamp(1.0, dend) which places the current clamp at soma(1) not dend(1). The correct (link to docs) thing to do is: istim = h.IClamp(dend(1)) What's going on? The "dend" parameter you're sending in is ...

I assume you're referring to the Scalar Bistable Wave example in the reaction-diffusion documentation. My guess is that you're putting the entire code into a single Jupyter cell and rerunning. Should this work? Yes, but apparently it's remembering parts of the configuration from one run to the next ...

h.FInitializeHandler normally takes a function that is to be called whenever NEURON initializes; i.e. we would normally say def my_initializer(): # do stuff here... fih = h.FInitializeHandler(my_initializer) To handle situations where we want to always send the function an argument or arguments, ins...

I pushed a version that supports extracellular diffusion to the development branch at http://github.com/ramcdougal/nrn . To try it, clone from there, compile, and run the code below. You should get two windows, one that shows a red square on a blue background (the initial condition), and one where d...