Search found 5785 matches

by ted
Mon Jun 29, 2020 12:57 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Arbitrary waveform
Replies: 1
Views: 312

Re: Arbitrary waveform

I used NMODL to generate the sine and biphasic square wave stimulus waveforms for three reasons: 1. properly written NMODL code "plays well" with adaptive integration 2. by exposing parameters but hiding implementational details, an NMODL-specified waveform generator offers the greatest convenience ...
by ted
Mon Jun 29, 2020 12:42 pm
Forum: NEURON + Python
Topic: Does the usage of the Shape may affect mV readouts?
Replies: 5
Views: 419

Re: Does the usage of the Shape may affect mV readouts?

Before commenting I will need to see this for myself. The model authors describe more than one way to launch the model. Exactly what did you do?
by ted
Mon Jun 29, 2020 11:51 am
Forum: Hot tips
Topic: NEURONS v is different than mine
Replies: 1
Views: 378

Re: NEURONS v is different than mine

At first I wrote one of the models into a single mod file I don't know anything about your expertise with NEURON or NMODL, but I do know that 1. Most user-written code contains errors, especially NMODL code. 2. All but the most trivial code has bugs. The only question is whether the effect of any p...
by ted
Fri Jun 26, 2020 10:33 am
Forum: NEURON hacks
Topic: Using NetCon where voltage is not the threshold variable
Replies: 3
Views: 1994

Re: Using NetCon where voltage is not the threshold variable

The NetCon class is useful for spike-triggered synaptic communication, in which it is often reasonable to assume that presynaptic details can be ignored. Signaling that is continuous in time cannot be properly represented with a NetCon. Continuous transmitter release can be implemented with NMODL's ...
by ted
Tue Jun 23, 2020 4:29 pm
Forum: NEURON + Python
Topic: ampanmda mod file working with AlphaSynapse
Replies: 7
Views: 1158

Re: ampanmda mod file working with AlphaSynapse

I would like to have more control over the EPSP shape and parameters, which the NetStim module doesn't offer me. In NEURON, a synaptic mechanism does not perturb membrane potential directly. It generates a current or a current + conductance change, which interacts with the electrical properties of ...
by ted
Mon Jun 22, 2020 11:54 pm
Forum: NEURON + Python
Topic: Error recording channel current by passing string to Vector.record
Replies: 3
Views: 333

Re: Error recording channel current by passing string to Vector.record

The problem is that Vector.record doesn't accept a string as its argument--it wants something that the parser recognizes to be a recordable variable. If you are determined to continue on this path, as an experiment you might see if Vector.record(eval(somestring)) succeeds; if it doesn't, you could t...
by ted
Mon Jun 22, 2020 10:45 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Maximum frequency of current stimulation
Replies: 3
Views: 279

Re: Maximum frequency of current stimulation

Where did you get the idea that NMODL controls t or dt? Did you read that somewhere? I ask because there's all kinds of nonsense in print and online, and if there's rubbish somewhere about NEURON, we need to know about it in order to be able to deal with it effectively. t and dt are built-in variabl...
by ted
Thu Jun 18, 2020 11:28 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Maximum frequency of current stimulation
Replies: 3
Views: 279

Re: Maximum frequency of current stimulation

However, when I plot the Curren injection profile, it looks like NEURON cannot follow MHz speed due to the fixed time step(dt) value. So make dt smaller. If you only want to satisfy the Nyquist criterion, 5e-4 ms would be sufficient. If you really want the sampled current to approximate a sine wave...
by ted
Wed Jun 17, 2020 9:22 pm
Forum: Other questions
Topic: vector.play memory efficiency
Replies: 4
Views: 335

Re: vector.play memory efficiency

Good. Presumably you are using a point process of some kind as the synaptic mechanism. I will need to see its NMODL source code--is that available online, or would you prefer to email it to me
ted dot carnevale at yale dot edu
by ted
Wed Jun 17, 2020 5:35 pm
Forum: Other questions
Topic: vector.play memory efficiency
Replies: 4
Views: 335

Re: vector.play memory efficiency

The correct answer to your question depends on exactly what you are trying to do. Do you have a sampled time course of synaptic conductance (either from a real experiment, or precomputed) that you want each synaptic instance to follow (give or take an instance-specific scale factor)? Or do you have ...
by ted
Fri Jun 05, 2020 5:45 pm
Forum: UNIX/Linux
Topic: .mod files compilation issues
Replies: 4
Views: 2483

Re: .mod files compilation issues

I installed NEURON on home directory. 0. Where did you get whatever you used to install NEURON? 1. Did you install from source code, or did you use a binary installer? 2. What is the complete path to where you installed NEURON? Example: a user named sam will have a home directory with path /home/sa...
by ted
Sun May 31, 2020 12:02 pm
Forum: Getting started
Topic: Represent images/movies in NEURON simulator
Replies: 2
Views: 1213

Re: Represent images/movies in NEURON simulator

Read about the PlotShape class's hinton() method, which is effective but not fancy. Warning: NetStim doesn't have a variable that can be used by PlotShape.hinton()
by ted
Sun May 31, 2020 11:47 am
Forum: Modeling networks
Topic: How to model synaptic activation using NetCon
Replies: 1
Views: 2163

Re: How to model synaptic activation using NetCon

If all you need is a single activation of an even-driven synapse, there's no need for a presynaptic cell. Just create the NetCon by (in hoc) objref nil, nc nc = new NetCon(nil, target) or (in Python) nc = h.NetCon(None, target) Then use the NetCon class's .event() method to specify the event deliver...
by ted
Sat May 30, 2020 2:02 am
Forum: NEURON + Python
Topic: range morphology and mechanism syntax for sections in python
Replies: 9
Views: 1496

Re: range morphology and mechanism syntax for sections in python

It looks like the answer is that you are allowed to do as fine grained an assignment as you want, but it will silently fail and implicitly assign to the nearest normalized segment position instead. Is this correct? No. It's what should be expected of a multicompartmental model. If you access a rang...