Search found 145 matches

by ramcdougal
Mon Apr 22, 2019 4:49 pm
Forum: UNIX/Linux
Topic: No module named hoc37
Replies: 10
Views: 112

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: 214

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: 217

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: 226

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: 533

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: 704

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: 704

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: 599

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: 21028

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: 1613

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: 1613

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: 1411

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...
by ramcdougal
Mon Aug 27, 2018 9:24 pm
Forum: Anatomically detailed models
Topic: area() function -- stylized method -- 3d-method
Replies: 4
Views: 924

Re: area() function -- stylized method -- 3d-method

There is some discussion about how segment areas and volumes are calculated at: https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/topology/geometry.html#d-specification-of-geometry To say what hines said another way: in your first case, you're defining a tapered shape while the...
by ramcdougal
Mon Aug 27, 2018 8:07 pm
Forum: Reaction-diffusion in NEURON
Topic: Reaction-Diffusion in HOC
Replies: 5
Views: 16777

Re: Reaction-Diffusion in HOC

Most likely that means that either Python is not installed, or it is installed but NEURON can't connect to it (likely a path issue). You're free to program NEURON models in HOC or Python, but to use the rxd module, Python must be installed and loadable by NEURON To check for this, check the return v...
by ramcdougal
Fri Aug 24, 2018 12:38 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Ineffective simulation with small duration current injection
Replies: 2
Views: 773

Re: Ineffective simulation with small duration current injection

Are you using a fixed time step or variable? I assume variable step will choose time points at the beginning and end of each current change... And thus you would see the current injection having an effect. If fixed, what is dt? Note that for fixed step, the default timestep (0.025 ms) is longer than...