Search found 5895 matches

by ted
Wed May 12, 2021 10:50 am
Forum: General questions and discussions about computational neuroscience
Topic: Getting started. Again.
Replies: 3
Views: 34

Re: Getting started. Again.

WRT NEURON, feel free to keep reading through at least chapter 9. Supplement that with the articles listed at https://neuron.yale.edu/neuron/publications/biblio (that list needs to be updated to include articles from the past 3 years, but it already contains enough papers to keep you busy for a whil...
by ted
Tue May 11, 2021 11:36 pm
Forum: General questions and discussions about computational neuroscience
Topic: Getting started. Again.
Replies: 3
Views: 34

Re: Getting started. Again.

Welcome, physicist. The center of NEURON's domain of utility is mechanistic modeling of biological neurons and networks in which the complex anatomical and biophysical properties of cells (including but not limited to ion channels) and the interconnections between them are important. NEURON models c...
by ted
Tue May 11, 2021 10:16 am
Forum: Other questions
Topic: Discrepancy between tvec and vector
Replies: 2
Views: 29

Re: Discrepancy between tvec and vector

Roundoff error is your enemy. You have to rely on the standard run system to decide when the simulation ends, but you're using the Vector class's indgen method to fill the t vector. Instead, use Vector.record to capture t, and the resulting recorded t vector will be the same length as the v vectors.
by ted
Tue May 11, 2021 12:38 am
Forum: NEURON + Python
Topic: silencing netstim during simulation.
Replies: 2
Views: 39

Re: silencing netstim during simulation.

The following if statement gives a syntax error, what is wrong with it? The clue does not lie in the code excerpt that you provided. What was the complete error message? But whatever is wrong with the if statement's syntax, the code excerpt contains several other errors. 1. The variable name $ns do...
by ted
Mon May 10, 2021 3:03 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Questions about the extracellular mechanism and the syntax of NMODL
Replies: 4
Views: 108

Re: Questions about the extracellular mechanism and the syntax of NMODL

It assumes that the extracellular medium is linear and not dispersive--in other words, the medium is purely resistive. Which implies that the extracellular potential at any point at any instant in time is proportional to the stimulus current at that time. The proportionality factor, which is called...
by ted
Fri May 07, 2021 3:30 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: mod file CVODE compatibility
Replies: 12
Views: 8045

Re: mod file CVODE compatibility

Could you suggest ways to make this model work with variable time step. In the Programmer's Reference read the general comments under the heading CVode at https://www.neuron.yale.edu/neuron/static/py_doc/simctrl/cvode.html#cvode In particular note the fourth paragraph which starts with The two majo...
by ted
Fri May 07, 2021 12:02 pm
Forum: Other questions
Topic: Axial currents at branch points
Replies: 4
Views: 82

Re: Axial currents at branch points

It's the notion of axial current breaking down at branch points that I didn't really understand The originator of the discussion thread to which you refer was "trying to measure the axial current between every segment in an object." Presumably that person's aim was to determine the curren...
by ted
Fri May 07, 2021 11:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Questions about the extracellular mechanism and the syntax of NMODL
Replies: 4
Views: 108

Re: Questions about the extracellular mechanism and the syntax of NMODL

I am trying to initially compute the potential of the neuron segments by COMSOL and then insert the data I produced into this code. Then in what variable (ex_xtra or er_xtra), should I insert the data of potential I've computed? You don't. xtra is based on transfer resistance between the stimulatin...
by ted
Thu May 06, 2021 11:42 am
Forum: Other questions
Topic: Axial currents at branch points
Replies: 4
Views: 82

Re: Axial currents at branch points

the notion of breakpoint at branch points (mentionned in post "recording axial current") still remain really confusing for me To me the most confusing thing is that the word "breakpoint" doesn't appear anywhere in the discussion thread titled recording axial current https://www....
by ted
Wed May 05, 2021 6:37 pm
Forum: NEURON hacks
Topic: Document related to NMODL
Replies: 1
Views: 98

Re: Document related to NMODL

net_send(), flag, WATCH, and FOR_NETCONS are not discussed in the hoc or Python documentation because they are features of NMODL, not of hoc or Python. net_send() and flag To learn about net_send() and flag read Discrete event simulation in the NEURON environment. Hines, M. L., and Carnevale N. T. N...
by ted
Mon May 03, 2021 4:05 pm
Forum: NEURON + Python
Topic: Correcting poor code design
Replies: 3
Views: 109

Re: Correcting poor code design

One writes code the way one writes anything else. In this particular case, start by printing on a small sheet of paper the incremental revision and testing algorithm, and the four step sequence I mentioned, and tape it to your desktop or your monitor. Get a sheet of paper and a pencil and start writ...
by ted
Mon May 03, 2021 3:54 pm
Forum: Modeling networks
Topic: How to activate network by synaptic mini current after time 50 ms when all network cells get silent
Replies: 5
Views: 156

Re: How to activate network by synaptic mini current after time 50 ms when all network cells get silent

I implemented an artificial spiking cell class called Autogoad. A zip file containing its mod file plus two demonstration programs is downloadable from https://www.neuron.yale.edu/ftp/ted/neuron/autogoad.zip Autogoad has two parameters: delay and interval. An Autogoad instance ignores inputs until t...
by ted
Mon May 03, 2021 12:10 pm
Forum: NEURON + Python
Topic: Correcting poor code design
Replies: 3
Views: 109

Re: Correcting poor code design

The GUI is a great way to get a lot done quickly, but it can become cumbersome to deal with all of those graphs and panels that are so easy to spawn. A good way to maintain sanity is to apply the principles of incremental revision and testing and modular code organization. Incremental revision and t...
by ted
Mon May 03, 2021 11:20 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Questions about the extracellular mechanism and the syntax of NMODL
Replies: 4
Views: 108

Re: Questions about the extracellular mechanism and the syntax of NMODL

could you please tell me the specific meaning of ex_xtra and er_xtra? Also with ex_xtra and er_xtra, which variable stores the extracellular potential? Read items 1 and 2 in the COMMENT block at the very start of the file. tell me the difference between RANGE, GLOBAL, and POINTER A RANGE variable m...
by ted
Thu Apr 29, 2021 1:11 am
Forum: Modeling networks
Topic: How to activate network by synaptic mini current after time 50 ms when all network cells get silent
Replies: 5
Views: 156

Re: How to activate network by synaptic mini current after time 50 ms when all network cells get silent

For instance last spike was generated by any network cell at 500 ms, I want to give synaptic current at 550 ms. OK, that should be doable with a bunch of NetCons (one for every cell in the network) and a single "artificial spiking cell." Here's what I suggest. Every cell in your network w...