Search found 5136 matches

by ted
Tue Feb 20, 2018 5:23 pm
Forum: Getting started
Topic: Peak duration
Replies: 3
Views: 111

Re: Peak duration

Don't even bother. NMODL is not well suited to that task. Develop your own code in Python or hoc that identifies each spike and determines its half width. That will involve many design decisions (especially if the spikes vary in amplitude, or if there is much subthreshold fluctuation of membrane pot...
by ted
Fri Feb 16, 2018 9:39 am
Forum: UNIX/Linux
Topic: Error in MOD compilation with a Slurm script
Replies: 3
Views: 81

Re: Error in MOD compilation with a Slurm script

nrnivmodl is a standalone executable, independent of NEURON's computational engine which is used to execute simulations. I'd expect that compilation of mod files should just work, period, unless your sbatch script does something to PATH that prevents nrnivmodl from finding a library that it needs.
by ted
Fri Feb 16, 2018 9:30 am
Forum: NEURON + Python
Topic: Accessing extracellular mechanism variables from Python
Replies: 12
Views: 3174

Re: Accessing extracellular mechanism variables from Python

The problems of setting and evaluating extracellular variables have been fixed. http://www.neuron.yale.edu/hg/neuron/nrn/rev/90f95519f23e Note that python requires explicit index syntax for vext, xg, xraxial,and xc to specify which extracellular layer (0, 1) is referenced. This link doesn't seem to...
by ted
Thu Feb 15, 2018 9:37 am
Forum: Hot tips
Topic: Extracellular stimulation and recording
Replies: 2
Views: 9583

Re: Extracellular stimulation and recording

Clever, but you missed this implementation of extracellular recording: Parasuram H, Nair B, D`Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational modeling of single neuron extracellular electric potentials and network Local Field Potentials using LFPsim Front. Comput. Neurosci. 10:65 https://...
by ted
Mon Feb 12, 2018 2:25 pm
Forum: NEURON + Python
Topic: Updating extracellular values for all segments!
Replies: 7
Views: 83

Re: Updating extracellular values for all segments!

After updating NEURON it is ALWAYS necessary to recompile mod files.
by ted
Thu Feb 08, 2018 4:40 pm
Forum: MSWin
Topic: NEURON and Python Installation
Replies: 1
Views: 84

Re: NEURON and Python Installation

The developers of PyNEURON would be whom to ask for support of PyNEURON.
by ted
Tue Feb 06, 2018 11:25 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Direction of current in point process
Replies: 2
Views: 72

Re: Direction of current in point process

NEURON uses the standard sign convention that neurophysiologists do. A NONSPECIFIC_CURRENT is just a transmembrane ionic current that is not attributed to a particular ionic species. It follows the same, time-honored sign convention that every other transmembrane current does--depolarizing current i...
by ted
Mon Feb 05, 2018 9:40 am
Forum: Other questions
Topic: Emit different types of spikes from a single cell
Replies: 8
Views: 105

Re: Emit different types of spikes from a single cell

* Is it possible to send an individual event down selected NetCons All active NetCons that share a given threshold detector will respond to a threshold crossing by placing events in the event queue that will be delivered to their targets after the user-specified delays. Whether or not a NetCon is a...
by ted
Sun Feb 04, 2018 10:29 pm
Forum: NEURON + Python
Topic: xpanel between python and hoc
Replies: 3
Views: 106

Re: xpanel between python and hoc

I have emailed you a zip file that contains source code that I hope will give you some useful idioms for using NEURON's GUI from Python. Let me know if you have more questions about this. In the meantime, for the benefit of other readers who may stumble across this thread, here is a list of some of ...
by ted
Fri Feb 02, 2018 11:46 pm
Forum: OS X
Topic: libnrnpython3 and libnrnpython2 on High Sierra
Replies: 13
Views: 973

Re: libnrnpython3 and libnrnpython2 on High Sierra

Moderator's note: The Forum's entropy is high enough already without the kind of thread fragmentation that results when users make multiple posts about the same problem. HoodyE90's post from earlier today, entitled Neuron 7.5 on MacOS High Sierra Problems has now been deleted. Here is the unique co...
by ted
Fri Feb 02, 2018 11:37 pm
Forum: Other questions
Topic: Emit different types of spikes from a single cell
Replies: 8
Views: 105

Re: Emit different types of spikes from a single cell

Progress in this discussion will be quicker if you now read the Programmer's Reference documentation about the NetCon class
https://www.neuron.yale.edu/neuron/stat ... etcon.html
Then we can pick up with whatever questions you may still have.
by ted
Fri Feb 02, 2018 12:11 am
Forum: Other questions
Topic: Emit different types of spikes from a single cell
Replies: 8
Views: 105

Re: Emit different types of spikes from a single cell

NEURON has no notion of "spike" as such, let alone "kind of spike." It has events. Spike-triggered synaptic transmission is implemented by using an instance of the NetCon class to couple a presynaptic "spike source" to a postsynaptic target. The presynaptic element may be a biophysical model cell or...
by ted
Thu Feb 01, 2018 12:05 pm
Forum: Other questions
Topic: Emit different types of spikes from a single cell
Replies: 8
Views: 105

Re: Emit different types of spikes from a single cell

would it be possible (including nasty hacks) to get Neuron to emit different types of spikes from a single cell
You mean in the course of the same simulation?
by ted
Wed Jan 31, 2018 9:28 am
Forum: Getting started
Topic: How to load and replace hoc files within a loop
Replies: 4
Views: 65

Re: How to load and replace hoc files within a loop

The main problem is how to clean up "top level" user-created variables (user-created variables, including objects, that are not embedded in an object instance). The only way to make sure that one can destroy all user-created variables happens is to embed all user-written code in an object. I know on...
by ted
Tue Jan 30, 2018 9:22 pm
Forum: Getting started
Topic: How to load and replace hoc files within a loop
Replies: 4
Views: 65

Re: How to load and replace hoc files within a loop

The problem is how to "clean up" after each simulation. You can't simply load the new model cell's specification and assume that stuff left over from the previous model cell will not interfere. The way to prevent such problems is to execute a set of independent simulations. This can be done by takin...