Search found 5785 matches

by ted
Thu Sep 08, 2005 10:45 am
Forum: Other questions
Topic: Total transmembrane current for segments
Replies: 5
Views: 6652

First please run this test: Make a single compartment model, insert pas and extracellular, apply an IClamp that delivers a current pulse, and verify that (i_pas + i_cap)*area(0.5) equals i_membrane*area(0.5). You might want to plot the difference between these two calculations of total membrane curr...
by ted
Wed Sep 07, 2005 1:08 pm
Forum: Other questions
Topic: Good reference on matrix-based numerical simulation
Replies: 3
Views: 4402

Vlach and Singhal

This is my favorite book on the subject:
Vlach, J., and Singhal, K.
Computer Methods for Circuit Analysis and Design
Wiley, 1983

On amazon.com I see that it is now published by Van Nostrand Reinhold and
lists for $215 (ouch!), but used copies are available and well worth the price.
by ted
Wed Sep 07, 2005 11:20 am
Forum: Anatomically detailed models
Topic: distance measurement
Replies: 5
Views: 8020

Re: Excluding the obvious

Raj raised a very good point. I should also mention that many morphometric reconstructions look beautiful in the xy plane, but just rotate 90 deg around the y axis and you discover that the z axis data contain a bunch of artifc You might want to try NEURON's Impedance tools, which, among other thing...
by ted
Wed Sep 07, 2005 10:53 am
Forum: Anatomically detailed models
Topic: distance measurement
Replies: 5
Views: 8020

Section access

This is a "good" example of abuse of the access keyword, even if the code works. NEURON has a "section stack," and the currently accessed section is governed by what is on the top of that stack. So far so good. The problem is that some actions can have side-effects on the stack, the result being tha...
by ted
Tue Sep 06, 2005 6:01 pm
Forum: Anatomically detailed models
Topic: Reducing complex models to equivalent cables
Replies: 9
Views: 10907

Re: nseg

The above code runs, but whenever I use a value of nseg that is not equal to 1, it crashes. What am I missing here? Beats the heck out of me why it runs at all. This line (x) ratio(x)" is mangled and should have generated an error message, but maybe it's flashing by too fast to be seen. Until you'r...
by ted
Tue Sep 06, 2005 10:03 am
Forum: Modeling networks
Topic: How to compile a self-defined integrate-fire MOD file?
Replies: 5
Views: 6827

The Gillies & Sterratt tutorial is very good, but if you're planning to do
serious NMODL development work, you should browse
Adding new mechanisms and functions to NEURON
https://www.neuron.yale.edu/phpBB2/viewforum.php?f=16
especially the post entitled
Where to learn about mod files and NMODL
by ted
Mon Sep 05, 2005 4:06 pm
Forum: Other questions
Topic: changing ena
Replies: 1
Views: 3095

Specifying iionic concentrations or equilibrium potentials

Good question. The answer is the same as the answer to
How can I control the extracellular environment?
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=42
by ted
Mon Sep 05, 2005 10:34 am
Forum: Hot tips
Topic: Which editing program to use?
Replies: 0
Views: 3952

Which editing program to use?

Not MicroSoft Word (Clippy, say it isn't true!).

Suggestions posted to the NEURON Forum include NoteTab, CREdit, and emacs--see
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=148

Here are some recent suggestions for OS X
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=874
by ted
Mon Sep 05, 2005 10:27 am
Forum: Getting started
Topic: plotting total cell current
Replies: 1
Views: 3887

current units for point processes vs. distributed mechanisms

Point processes report current in absolute units (nA), whereas distributed mechanisms report current density (mA/cm2). See https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=161 for more information. Note: the values are numerically equal if the surface area is 100um2. That's why the GUI's NEURON Ma...
by ted
Mon Sep 05, 2005 10:12 am
Forum: Hot tips
Topic: Extracellular stimulation and recording
Replies: 4
Views: 25198

Extracellular stimulation and recording

One approach to extracellular stimulation is to introduce, into the cable equation, a current term that is proportional to the second spatial derivative of the extracellular field. This is essentially the "activating function" method described by Rattay Rattay F (1986): Analysis of models for extern...
by ted
Mon Sep 05, 2005 10:11 am
Forum: Other questions
Topic: Total transmembrane current for segments
Replies: 5
Views: 6652

extracellular stimulation and recording

i_membrane is available after inserting the extracellular mechanism. Read about it here http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/mech.html#extracellular You might find this http://www.neuron.yale.edu/ftp/ted/neuron/extracellular_stim_and_rec.zip helpful. It contains complete ...
by ted
Sun Sep 04, 2005 1:37 pm
Forum: Hot tips
Topic: GUI tools: Shape Name
Replies: 0
Views: 4544

GUI tools: Shape Name

Every NEURON user probably knows about the "builders" (Cell*, Channel*, Network*, LinearCircuit*), and ModelView is also becoming more widely used. However, the GUI has many other tools and features that are easily overlooked, but which can be quite helpful from time to time. One is the Shape Name t...
by ted
Sun Sep 04, 2005 1:09 pm
Forum: Hot tips
Topic: How to change parameters during a simulation
Replies: 1
Views: 10637

How to change parameters during a simulation

How to change a model's parameters in the course of a simulation is a common problem. One way is to use the Vector class's play method. This example uses Vector play with interpolation to make celsius change "continuously" from 6.3 to 20 deg C over the course of 100 ms. Yes, that's unrealistically f...
by ted
Sat Sep 03, 2005 9:57 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: programatically changing the temperature
Replies: 8
Views: 11646

event-driven parameter changes

3. celsius, or any other parameter, can be made to jump abruptly from one temperature to another by using FInitializeHandler and cvode.event(), but that's a different story . . . I know somebody's going to ask sooner or later, so here's an example that uses the event delivery system to generate a s...