Search found 173 matches

by ramcdougal
Fri Mar 01, 2019 10:00 am
Forum: MSWin
Topic: Windows 10 install problem. Path issue?
Replies: 1
Views: 1214

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: 867

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: 1420

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: 1998

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: 1998

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: 1236

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: 23530

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: 3006

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: 3006

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: 2093

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: 1771

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: 17866

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: 1308

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...
by ramcdougal
Wed Aug 22, 2018 6:13 am
Forum: NEURON + Python
Topic: Not able to run simulation more than once from a NEURON+Python script
Replies: 4
Views: 2390

Re: Not able to run simulation more than once from a NEURON+Python script

Doesn't solve the mystery, but...

Assuming the morphology is not changing with successive runs, you could load it once before entering the loop, and see this particular issue entirely
by ramcdougal
Mon Aug 13, 2018 1:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Computational Optogenetics: modelling ChR2 in NMODL
Replies: 2
Views: 1394

Re: Computational Optogenetics: modelling ChR2 in NMODL

You can probably do what you want by using Vector.play . In brief, Vector.play allows you to use two Vectors (one listing time points and one with the values) to control an arbitrary memory location (e.g. a current, or in your case a variable in a MOD file). Example that plays a stimulus into the in...