Search found 5470 matches

by ted
Fri Apr 19, 2019 10:24 am
Forum: Other tools
Topic: Just a test
Replies: 1
Views: 19638

Re: Just a test

Another test
by ted
Wed Apr 10, 2019 4:55 pm
Forum: Optimization
Topic: Optimization of single cell models
Replies: 3
Views: 65

Re: Optimization of single cell models

If the only aspect of the oscillation that you want to change is average membrane potential, do what I suggested in my previous post.
by ted
Mon Apr 08, 2019 9:39 am
Forum: Other questions
Topic: short duration biphasic current stimulation
Replies: 6
Views: 112

Re: short duration biphasic current stimulation

SEClamp is extremely simple--just a voltage source in series with a resistance.
by ted
Sat Apr 06, 2019 12:07 am
Forum: Other questions
Topic: Integrate-and-fire model with passive dendrite
Replies: 1
Views: 61

Re: Integrate-and-fire model with passive dendrite

Use the CellBuilder to make a model cell with two sections called soma and dendrite. On the Geometry page, specify the L and diam of these sections, but leave each section's nseg == 1. Use the Biophysics page to insert pas and set appropriate values for Ra, cm, g_pas, and e_pas. If you've never used...
by ted
Fri Apr 05, 2019 1:12 pm
Forum: Optimization
Topic: Optimization of single cell models
Replies: 3
Views: 65

Re: Optimization of single cell models

I don't know what it means to say that an oscillating model has a resting potential (unless the model's phase space has a feature that separates trajectories that collapse to a stable node from trajectories that don't). There are many ways to shift the resting potential of a model that has a resting...
by ted
Fri Apr 05, 2019 1:05 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 35
Views: 8108

Re: Installation problem Neuron

stephanmg: that post is more than half a year old. Chances are that the "library deprecated out of existence" issue has been resolved. You could try to confirm that by searching the commits at https://github.com/neuronsimulator/nrn/commits/master, or just get the most recent source code and see what...
by ted
Wed Apr 03, 2019 4:05 pm
Forum: Other questions
Topic: short duration biphasic current stimulation
Replies: 6
Views: 112

Re: short duration biphasic current stimulation

The short biphasic current does produce a monophasic pulse of membrane potential. And, just like an extracellular stimulus, it does not affect the model's equations (doesn't introduce a shunting conductance). A voltage clamp has a _very_ low source impedance, and is not electrically equivalent to ex...
by ted
Tue Apr 02, 2019 11:52 am
Forum: The GUI
Topic: Adding Ion Channels
Replies: 1
Views: 65

Re: Adding Ion Channels

"Block Na Channel" and "Unblock Na Channel" are not part of NEURON. Besides, they're just labels in a graphical user interface, not the names of parameters. Some third party created the "action potential" folder and is responsible for its contents. Contact that person and see if he or she will share...
by ted
Thu Mar 28, 2019 1:07 pm
Forum: MSWin
Topic: Neuron File Association
Replies: 1
Views: 97

Re: Neuron File Association

I'm not aware of a specific NEURON installation option that does this, but searching the web for
windows 10 file association for all users
finds lots of hits. If one of these works for you, perhaps you could post it here so others can benefit.
by ted
Thu Mar 28, 2019 12:49 pm
Forum: Other questions
Topic: short duration biphasic current stimulation
Replies: 6
Views: 112

Re: short duration biphasic current stimulation

There are two problems. The first problem is that your model cell is not very excitable. If you reduce the amplitude of the biphasic stimulus to 0 (by executing run_exp(0)), then attach an IClamp with del 1, dur 0.1, you can do some exploratory simulations. I'll send you a session file that recreate...
by ted
Thu Mar 28, 2019 10:42 am
Forum: Getting started
Topic: Apical/Basal dendrites and Axon Collateral
Replies: 1
Views: 83

Re: Apical/Basal dendrites and Axon Collateral

A computational model is an implementation of a conceptual model (a hypothesis). Some modelers' conceptual models of pyramidal cells reduce the entire cell to a "point cell" that has no spatial extent. No dendrites at all. Some conceptual models of pyramidal cells preserve all details of the branche...
by ted
Thu Mar 28, 2019 10:29 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 853

Re: Morphology and AP generation

Ah, yes--I generally import both h and gui from neuron import h, gui Importing gui causes stdrun.hoc to be loaded, so lambda_f is declared and geom_nseg() succeeds. But it also loads several other files and brings up the NEURON Main Menu toolbar. If you don't want that to happen, but you do want you...
by ted
Wed Mar 27, 2019 9:43 am
Forum: Other questions
Topic: short duration biphasic current stimulation
Replies: 6
Views: 112

Re: short duration biphasic current stimulation

I haven't seen anything like that. It will be necessary for me to be able to reproduce the phenomenon with the same code you are using. If you zip it up (hoc, Python, ses, NMODL, whatever else is needed) and email it to ted dot carnevale at yale dot edu, I'll see what I can find out and be able to a...
by ted
Wed Mar 27, 2019 12:17 am
Forum: General questions and discussions about computational neuroscience
Topic: Morphology and AP generation
Replies: 17
Views: 853

Re: Morphology and AP generation

I'm not a Jupyter user, so I just ran some tests with Python. After h.load_file("fmc3_1") I tried for sec in h.allsec(): for seg in sec: print(seg) several times and it worked correctly all times. Also tried printing sec and seg.x, and h.secname() and seg.x several times. Each of these produced the ...
by ted
Mon Mar 25, 2019 4:12 pm
Forum: NEURON Announcements
Topic: 2019 NEURON Summer Course
Replies: 0
Views: 162

2019 NEURON Summer Course

What and When: The 2019 NEURON Summer Course is a six day hands-on course about computational modeling with NEURON. It will start at 9 AM on Monday, June 10, and end at 5 PM on Saturday, June 15, 2019. This course will present what you need to know to use NEURON to model individual neurons and netw...