Search found 5936 matches

by ted
Mon May 24, 2021 10:59 am
Forum: The GUI
Topic: GUI bug in netbuilder?
Replies: 4
Views: 226

Re: GUI bug in netbuilder?

when I tried to save the NetBuilder and assorted paraphernalia to a .ses file, I got an endless loop of seg fault errors
I don't like any of this. Can you uninstall NEURON completely, then install the latest version (8.0) from www.neuron.yale.edu? You'll have to recompile your .mod files.
by ted
Mon May 24, 2021 10:06 am
Forum: The GUI
Topic: GUI bug in netbuilder?
Replies: 4
Views: 226

Re: GUI bug in netbuilder?

It looks like you connected the spike source (a NetStim) to a valid target (an Exp2Syn), but . . . The line stays in place, but never becomes thick, and the help prompt never changes. Yes, those changes should have happened. What happens if you simply resize the window a bit? What version of NEURON ...
by ted
Fri May 21, 2021 2:04 pm
Forum: Modeling networks
Topic: How to activate network by synaptic mini current after time 50 ms when all network cells get silent
Replies: 11
Views: 713

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

If you walk through the code carefully after being away from it for a couple of days, you might see that the problem is with the statement that creates the NetCons that drive the agcell pyag = new NetCon(NW_list.o(i), agcell, 0, 1, .025) The "spike sources" in this statement are the elemen...
by ted
Thu May 20, 2021 3:26 pm
Forum: Getting started
Topic: Learning by recreating the HH model
Replies: 1
Views: 150

Re: Learning by recreating the HH model

How do I "lift the hood" and see what those built-in HH settings are? Examine the NMODL code for the hh mechanism. It's in hh.mod. I don't think you'll find hh.mod on your machine if you used one of NEURON's binary installers; if that's the case, download NEURON's source code https://gith...
by ted
Thu May 20, 2021 3:03 pm
Forum: Getting started
Topic: How are sections connected?
Replies: 5
Views: 276

Re: How are sections connected?

Would the input resistance be RA*2 Yes. can the time constant be defined as: tau = rmcm where rm is the specific membrane resistance of the compartment (in ohm cm2) and cm is the membrane capacitance of the compartment (in F)? No, since the resulting units are s/cm2. cm needs to be specific membran...
by ted
Thu May 20, 2021 2:23 pm
Forum: NetPyNE
Topic: LIF neuron model with GABA/AMPA/NMDA conductances
Replies: 4
Views: 225

Re: LIF neuron model with GABA/AMPA/NMDA conductances

Sent yesterday to your hw.ac.uk address at about 740 PM EDT (i.e. New York time).
by ted
Wed May 19, 2021 7:12 pm
Forum: NetPyNE
Topic: LIF neuron model with GABA/AMPA/NMDA conductances
Replies: 4
Views: 225

Re: LIF neuron model with GABA/AMPA/NMDA conductances

Based on my readings, I am supposed to build a point_process cell using the NMODL programming language. I don't know what your readings are, but good luck with implementing such an artificial spiking cell completely in NMODL. The easy ones have already been done. This a LIF neuron model with GABA/A...
by ted
Wed May 19, 2021 12:17 pm
Forum: Getting started
Topic: How are sections connected?
Replies: 5
Views: 276

Re: How are sections connected?

I understand the point that the elements are not in parallel, however I am still unclear as to how the total membrane capacitance can thus be calculated by the summation across segments/sections? Total membrane capacitance is total membrane capacitance, i.e. the integral over the surface of the cel...
by ted
Mon May 17, 2021 11:22 pm
Forum: Getting started
Topic: How are sections connected?
Replies: 5
Views: 276

Re: How are sections connected?

I would like to know how sections in the models are connected to each other, e.g. what the equivalent circuit would look like? Fig. 5.6D in The NEURON Book shows the equivalent circuit for a section that has nseg = 1. Its 0 and 1 ends are labeled clearly. Suppose you had two sections, both with nse...
by ted
Mon May 17, 2021 12:52 am
Forum: NEURON Announcements
Topic: 2021 NEURON Online Course
Replies: 4
Views: 1133

2021 NEURON Online Course

The 2021 NEURON Online Course will start on Thursday, June 3, 2021, and will meet Tuesdays and Thursdays thereafter until Tuesday, August 3. This course maps the first half of the NEURON Summer Course into a series of interactive online workshops about building and working with models of single neur...
by ted
Sat May 15, 2021 7:02 pm
Forum: General questions and discussions about computational neuroscience
Topic: Getting started. Again.
Replies: 6
Views: 428

Re: Getting started. Again.

the models used in NEURON I'm not quite sure what you mean. If you mean "how are the properties of biological neurons represented in mechanistic models of neurons implemented with NEURON" then chapters 3-5 of The NEURON Book are for you. What isn't covered in those chapters? Drug-receptor...
by ted
Wed May 12, 2021 10:50 am
Forum: General questions and discussions about computational neuroscience
Topic: Getting started. Again.
Replies: 6
Views: 428

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: 6
Views: 428

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: 172

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: 237

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...