Search found 6290 matches

by ted
Wed Apr 26, 2006 2:20 pm
Forum: Other questions
Topic: templated cells and shape name viewer
Replies: 4
Views: 4962

Not a waste of time at all. These discussions become part of the available documentation,
and very often address issues that haven't been covered elsewhere.
by ted
Wed Apr 26, 2006 12:12 pm
Forum: Other questions
Topic: templated cells and shape name viewer
Replies: 4
Views: 4962

Correct. A class definition that is written by the CellBuilder includes a public
procedure called position() that can be used to specify the location of any
cell instance. For example,

Code: Select all

objref pyr4
pyr4 = new L4pyr()
pyr4.position(10, 20, 30) // desired coords of 0 end of root section (soma)
by ted
Tue Apr 25, 2006 11:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How does NEURON calculate the membrane potential?
Replies: 3
Views: 9672

Re: How does NEURON calculate the membrane potential?

How does NEURON calculate the membrane potential? Numerical integration of the cable equation. See chapter 5 of The NEURON Book, or read Hines, M.L. and Carnevale, N.T. The NEURON simulation environment. In: The Handbook of Brain Theory and Neural Networks, 2nd ed, edited by M.A. Arbib. Cambridge, ...
by ted
Fri Apr 21, 2006 12:14 am
Forum: Getting started
Topic: reduced compartment model
Replies: 1
Views: 2837

The first and most important tool for reducing model complexity is judgement, guided by experience and a thorough knowledge of the experimental basis for the model in question. There have been a few papers on the topic of model simplification; you might start by reading this one: Bush, P.C. and Sejn...
by ted
Fri Apr 21, 2006 12:11 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Absolute refractory period for IntFire2
Replies: 1
Views: 3708

Offhand I can't think of a "deep reason" why a self event couldn't be used to create an IntFire2 variant that has an absolute refractory period. Unless something is judged to be of widespread interest, it generally won't be added to the standard distribution. That said, there are two avenu...
by ted
Thu Apr 20, 2006 11:53 pm
Forum: General questions and discussions about computational neuroscience
Topic: Threshold-Action potential
Replies: 1
Views: 7354

This thread was moved to "General questions . . . " because it does not pertain to
NEURON.

The Hodgkin-Huxley action potential does not have a threshold voltage. This was
established over 30 years ago, although I do not have a citation at hand.
by ted
Wed Apr 19, 2006 2:39 pm
Forum: NEURON Announcements
Topic: 2006 NEURON Simulator Meeting
Replies: 4
Views: 14574

NEURON Simulator Meeting update

Three more reasons to sign up for the NEURON Simulator Meeting, which will take place May 5-7 at the Center for Learning and Memory, University of Texas, Austin http://www.utexas.edu/neuroscience/NEURON2006/nsm2006.html 1. Space is still available, but you'll have to act quickly to take advantage of...
by ted
Wed Apr 19, 2006 10:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Extracellular stimulation giving problems
Replies: 1
Views: 2721

Test your program on a toy model that has simple topology.
Insert print statements at critical points in your code, to discover at what point the program
stops doing what it should.
by ted
Wed Apr 19, 2006 10:26 am
Forum: Other questions
Topic: Extracellular stimulation
Replies: 1
Views: 3061

Re: Extracellular stimulation

This is the correct approach:
assign e_extracellular values to the center of each compartment?
Every segment's membrane should be exposed to its own local extracellular potential.
by ted
Wed Apr 19, 2006 10:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: combining schemes
Replies: 7
Views: 6903

I don't think I can use the ChannelBuilder because (1) I need to include a Ca2+ accumulation mechanism Apply the principle of modular software design. Specify a Ca accumulation mechanism with NMODL, and specify the channel properties with a ChannelBuilder. (2) my ionic current equation is non-stand...
by ted
Tue Apr 18, 2006 4:55 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: calcium dependent inactivation function
Replies: 13
Views: 11787

Unfortunately I have to wrestle with all these currents and concentrations (CaL,CaN,CaT) Follow the recommendations stated above--see my msg that contains The place to start is with the calcium accumulation mechanism. This All calcium currents should USEION ca READ eca, cai WRITE ica ensures that w...
by ted
Tue Apr 18, 2006 1:47 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: calcium dependent inactivation function
Replies: 13
Views: 11787

Andrew Gillies and David Willshaw Membrane channel interactions underlying rat subthalamic projection neuron rhythmic and bursting activity J.Neurophysiology(2005) You mean this one? Andrew Gillies and David Willshaw Membrane Channel Interactions Underlying Rat Subthalamic Projection Neuron Rhythmi...
by ted
Tue Apr 18, 2006 10:19 am
Forum: Adding new mechanisms and functions to NEURON
Topic: calcium dependent inactivation function
Replies: 13
Views: 11787

No need to send the PDF. The citation will be sufficient. I probably already have the
paper, and if not, I will almost certainly be able to retrieve it for myself. I really prefer not
to have my mailbox fill up with emails that have giant attachments.
by ted
Mon Apr 17, 2006 7:17 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: calcium dependent inactivation function
Replies: 13
Views: 11787

Intracellular calcium levels were modelled in a sub-membrane shell with buffering and diffusion modelled as an exponential decay. With the equation (that includes the three currents) of the form: [ cai] ' =(Ilca+Inca+Itca)*c*(cai0-[cai])/tca c :is the conversion constant tca:the time constant of th...
by ted
Mon Apr 17, 2006 2:35 pm
Forum: Getting started
Topic: Rest Membrane Potential
Replies: 3
Views: 4371

first, i inject a current to reach membrane potential to a specific level, and after some delay.e,g 500ms, i use other ICamp current, to study the response of my model. That can work, if the time you wait is long enough (models that have ion accumulation mechanisms--especially calcium diffusion/pum...