Search found 148 matches

by ramcdougal
Thu Jun 06, 2019 10:25 am
Forum: Getting started
Topic: Accessing the current between extracellular layers
Replies: 6
Views: 130

Re: Accessing the current between extracellular layers

Are you trying to simulate ephaptic coupling or extracellular diffusion of ion concentrations in the extracellular space? There are currently at least two models in ModelDB that use NEURON for ephaptic coupling: http://identifiers.org/modeldb/3676 and http://identifiers.org/modeldb/240957 (The rxd m...
by ramcdougal
Sat May 18, 2019 2:38 pm
Forum: NEURON + Python
Topic: Adex neuron in neuron python
Replies: 5
Views: 190

Re: Adex neuron in neuron python

The literal translation is adapex=h.ADEX(0.5) Since this is technically a point process, the 0.5 means it gets associated with the middle of some section, the so called currently accessed section. This is fine, but in Python we can be more explicit about which section, here mysec: adapex=h.ADEX(myse...
by ramcdougal
Tue May 07, 2019 1:55 pm
Forum: Reaction-diffusion in NEURON
Topic: Questions about Calcium Waves in RxD
Replies: 2
Views: 178

Re: Questions about Calcium Waves in RxD

I've added a full working code (and the associated image output) to the calcium wave rxd tutorial page: https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave There's not much in the way of explanation yet, but hopefully after working through the rest of the existing tutorials ( https:/...
by ramcdougal
Mon Apr 22, 2019 4:49 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 10
Views: 541

Re: No module named hoc37

Two questions: Does NEURON work from a regular python prompt (i.e. not Spyder) What is the full NEURON part of your PYTHONPATH? Because of reasons NEURON installs two versions of the library. Only one has the "missing" file. In particular, on my machine the two paths are: /usr/local/nrn/lib/python/n...
by ramcdougal
Fri Mar 01, 2019 11:33 am
Forum: Reaction-diffusion in NEURON
Topic: USEION in mod files for RxD species I created
Replies: 3
Views: 323

Re: USEION in mod files for RxD species I created

Ted raises good points. The underlying issue though is that if you run the straightforward translation of that mod file, you'll get a maximum value of 1 (assuming your concentrations are below 1). Why 1? It has to do with the order of events during initialization: NEURON sets concentrations to 1 unl...
by ramcdougal
Fri Mar 01, 2019 10:00 am
Forum: MSWin
Topic: Windows 10 install problem. Path issue?
Replies: 1
Views: 343

Re: Windows 10 install problem. Path issue?

To fix, add the following two paths to your system PATH environment variable (for instructions on how to modify PATH, see https://www.architectryan.com/2018/03/17/add-to-the-path-on-windows-10/ ): c:\nrn\bin c:\nrn\mingw\usr\bin We've identified the source of the 1024 limit, and this should be fixed...
by ramcdougal
Mon Feb 18, 2019 4:57 pm
Forum: Reaction-diffusion in NEURON
Topic: RXD lower concentration limit?
Replies: 2
Views: 307

Re: RXD lower concentration limit?

This is likely due to a previously under-appreciated detail in the numerical methods used for 3D simulation. In particular, we use scipy.sparse.linalg.bicgstab with a tolerance of 1e-5 to solve a matrix problem. This should have been connected to the atol used elsewhere*, but it is not. For now, you...
by ramcdougal
Tue Dec 04, 2018 7:05 am
Forum: NEURON + Python
Topic: Using VecStim() with CVode on
Replies: 3
Views: 702

Re: Using VecStim() with CVode on

Adaptive integration chooses timesteps to constrain error.

In particular, unlike fixed step integration, it will adapt its timesteps to handle events at the time received and not shift them or group them.
by ramcdougal
Mon Nov 26, 2018 7:28 pm
Forum: NEURON + Python
Topic: Accessing inf_hh and tau_hh in the hh mechanism
Replies: 6
Views: 941

Re: Accessing inf_hh and tau_hh in the hh mechanism

Conceptually, you are correct. For memory reasons, however, NEURON's hh.mod doesn't actually store those values since they are only useful for computing one location at one time point. Instead, a GLOBAL value is used, meaning that there is only one memory location used for every spatial point (diffe...
by ramcdougal
Mon Nov 26, 2018 6:01 pm
Forum: NEURON + Python
Topic: Accessing inf_hh and tau_hh in the hh mechanism
Replies: 6
Views: 941

Re: Accessing inf_hh and tau_hh in the hh mechanism

Globals are accessed globally; i.e. through the h object:

Code: Select all

from neuron import h
soma = h.Section(name='soma')
soma.insert('hh')
print(h.htau_hh)
print(h.hinf_hh)
by ramcdougal
Wed Nov 14, 2018 5:05 pm
Forum: Reaction-diffusion in NEURON
Topic: maximum length for the name of a species?
Replies: 2
Views: 690

Re: maximum length for the name of a species?

What's happening is that NEURON currently assumes a limit on ion name lengths. You can see this without rxd in that the following two lines will crash NEURON: from neuron import h h.ion_register('x'*50, 0) If, as in your example code, you have a pure reaction-diffusion model (no ion channels) you ca...
by ramcdougal
Wed Oct 24, 2018 7:07 am
Forum: NEURON + Python
Topic: More NEURON + Python documentation
Replies: 6
Views: 21423

Re: More NEURON + Python documentation

Since this discussion, there had been a lot of work on the Python interface to make things cleaner, especially in NEURON 7.5 and 7.6. We're in the process of reworking the main NEURON Python tutorial: https://neuron.yale.edu/neuron/static/docs/neuronpython/index.html The draft revised pages (only th...
by ramcdougal
Thu Oct 11, 2018 3:01 pm
Forum: HNN: Human Neocortical Neurosolver
Topic: Installation Issues
Replies: 4
Views: 1843

Re: Installation Issues

I suggest trying the following to get NEURON to work:

Download and install the .deb from http://neuron.yale.edu

Then (to allow both Anaconda and your system Python to find NEURON) add the following to your ~/.bashrc:

Code: Select all

export PYTHONPATH=/usr/local/nrn/lib/python/:$PYTHONPATH
by ramcdougal
Tue Sep 18, 2018 10:16 pm
Forum: HNN: Human Neocortical Neurosolver
Topic: Installation Issues
Replies: 4
Views: 1843

Re: Installation Issues

Strictly speaking, the command on the installer's line 13 sudo apt install -y python3-pyqt5 python3-pip python3-pyqtgraph python3-opengl zlib1g-dev zlib1g zlibc libx11-dev mercurial bison flex automake libtool libxext-dev libncurses-dev python3-dev xfonts-100dpi cython libopenmpi-dev python3-scipy p...
by ramcdougal
Fri Sep 14, 2018 10:59 am
Forum: Reaction-diffusion in NEURON
Topic: Add term to RxD solution.
Replies: 2
Views: 1512

Re: Add term to RxD solution.

The bad news: The reaction-diffusion module rxd currently only directly supports reactions and diffusions. So you could add arbitrary local kinetics, but you'd have to modify the source to add the type of dynamics you describe. The good news: besides storing parameters, all of the changes would be c...