Search found 5988 matches

by ted
Mon Nov 08, 2021 11:20 pm
Forum: Modeling networks
Topic: How to model presynaptic voltage?
Replies: 7
Views: 249

Re: How to model presynaptic voltage?

Quite unique. Looks like something that was originally implemented for some non-NEURON simulation environment, or maybe some programming language. Was this originally published somewhere, or does it exist in some widely accessible code library? It must assume a very specific fixed time step, and it ...
by ted
Mon Nov 08, 2021 2:21 pm
Forum: Modeling networks
Topic: How to model presynaptic voltage?
Replies: 7
Views: 249

Re: How to model presynaptic voltage?

it has no NET_RECIEVE NET_RECEIVE. Isn't there an equivalent event-driven mechanism that you could use? How can I send an array (which contains the presynaptic potential of each time step) to the synapse (response to potential/voltage)? Are you inextricably committed to such an approach, i.e. havin...
by ted
Fri Nov 05, 2021 1:23 pm
Forum: Modeling networks
Topic: Spike-Time Dependent Plasticity in a parallel network
Replies: 4
Views: 7345

Re: Spike-Time Dependent Plasticity in a parallel network

tpre is the time of the most recent presynaptic spike.
tpost is the time of the most recent postsynaptic spike.
t is the current time.
by ted
Fri Nov 05, 2021 12:38 pm
Forum: General questions and discussions about computational neuroscience
Topic: Low Frequency Stimulation model
Replies: 3
Views: 318

Re: Low Frequency Stimulation model

whether the methods you prescribed would function for an AC electrode rather than a single direct current Think about the underlying physics and consider these questions: Given a conductive medium, what would make the electrical potential vary with position? What are the assumptions about the physi...
by ted
Thu Nov 04, 2021 1:21 pm
Forum: Other questions
Topic: Delaying channel blockers
Replies: 1
Views: 184

Re: Delaying channel blockers

There are several ways to implement a (computational) experimental protocol that involves parameter changes. One is to use the Vector class's play() method. Another is to use events to force parameter changes at specific times. See How to change parameters during a simulation in the Hot tips area of...
by ted
Thu Nov 04, 2021 12:10 pm
Forum: NEURON + Python
Topic: Time dependent NetCon weight
Replies: 1
Views: 158

Re: Time dependent NetCon weight

is it possible to implement a NetCon whose weight is time dependent. This is generally not what people want to do. Usually they want an event-driven point process whose response to an event will vary from event to event. The most typical case is synaptic plasticity, e.g. short term synaptic facilit...
by ted
Wed Nov 03, 2021 2:09 pm
Forum: NEURON hacks
Topic: Complex presynaptic cell
Replies: 3
Views: 398

Re: Complex presynaptic cell

Does this pertain to the hoc code used in your other post "added a synapse with python"
by ted
Wed Nov 03, 2021 2:04 pm
Forum: NEURON + Python
Topic: added a synapse with python
Replies: 1
Views: 176

Re: added a synapse with python

I get an error when trying to add the synapse. What are you doing to "add the synapse"? In addition, when I load the hoc file I can't load the morphology of the cell. Not sure what this means. As soon as you create an instance of either of the cell classes defined in your example code, th...
by ted
Fri Oct 29, 2021 1:23 pm
Forum: Other questions
Topic: Trying to use SectionRefs crashing the simulation.
Replies: 2
Views: 144

Re: Trying to use SectionRefs crashing the simulation.

Try getting something working on a real simple toy model with just a couple of sections and minimal membrane properties at the top level (not wrapped in a class definition). Use nothing but hoc at first. Then try calling it from python. After that, if your real application involves a section that be...
by ted
Thu Oct 28, 2021 1:43 pm
Forum: General questions and discussions about computational neuroscience
Topic: Low Frequency Stimulation model
Replies: 3
Views: 318

Re: Low Frequency Stimulation model

You've got the general idea. However 1. Every pass through the for i=0,50 loop overwrites the same objref (stimvec, which is synonymous with stimvec[0]). Consequently e_extracelluar will have the same value in all segments. 2. Code that uses whole numbers to iterate over segments doesn't scale well....
by ted
Wed Oct 27, 2021 11:02 am
Forum: NEURON hacks
Topic: Complex presynaptic cell
Replies: 3
Views: 398

Re: Complex presynaptic cell

Absolutely, but it requires executing user-written code. The Network Builder is a great tool for creating small prototype models that involve only a few cells. Several simplifying assumptions are built into it. One is that, if the presynaptic cell is a biophysical model cell (that is, has sections),...
by ted
Tue Oct 26, 2021 11:10 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Modifying cell capacitance (cm) via a mod file (also cai)
Replies: 2
Views: 329

Re: Modifying cell capacitance (cm) via a mod file (also cai)

Interesting problem. Regarding varying membrane capacitance: First see https://www.neuron.yale.edu/phpBB/viewtopic.php?p=15854#p15854 and the reply by Michael Hines. Then check out this entry in GitHub https://github.com/nrnhines/dcmdt . Finally, it might be useful to examine modeldb.yale.edu/264539...
by ted
Tue Oct 19, 2021 12:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2534

Re: undersampling curves

This note is primarily for others who may read this thread. Using NMODL for "data processing on the fly" raises several potential issues. 1. In this particular application, the sequence of execution of NMODL-specified mechanisms is important. Clearly all mechanisms that WRITE ica must be e...
by ted
Wed Oct 13, 2021 1:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 2534

Re: undersampling curves

I begin to see your problem. I thought you were working with some generic optimization library that you could just feed some postprocessed data after a simulation was complete. Instead, you're probably using

Code: Select all

xopen("fit.ses")
to recreate a Multiple Run Fitter, right?
by ted
Wed Oct 13, 2021 12:37 pm
Forum: NEURON + Python
Topic: Error running NEURON with embedded Python
Replies: 3
Views: 2824

Re: Error running NEURON with embedded Python

Thanks for following up with the fix for that!