Search found 5785 matches

by ted
Wed Sep 14, 2005 1:44 pm
Forum: Other questions
Topic: input to a netcon synapse from an external file
Replies: 5
Views: 7440

model of saturating AMPAergic synapse

Here's Listing 10.5 from The NEURON Book--the NMODL code for a saturating AMPAergic synaptic mechanism that works with the event delivery system. You may want to compare the PARAMETERs against those that Alain used in his original implementation, and change them if necessary. : ampa.mod : saturating...
by ted
Wed Sep 14, 2005 1:33 pm
Forum: Other questions
Topic: input to a netcon synapse from an external file
Replies: 5
Views: 7440

driving a synaptic mechanism with events at specified times

The straightforward way to do what you want is to exploit the NetCon class's event() method, which allows you to stuff events into the queue--see http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/netcon.html#event Here's an outline of the changes you need to make: 1. Translate...
by ted
Tue Sep 13, 2005 12:47 pm
Forum: Getting started
Topic: multi compartment model
Replies: 1
Views: 4295

Re: multi compartment model

Good questions. A good place to find the answers: go to NEURON's Documentation page http://www.neuron.yale.edu/neuron/docs and look under the heading Key papers about NEURON for this item "The NEURON Simulation Environment" An earlier paper with the same title, expanded from our first article in Neu...
by ted
Tue Sep 13, 2005 12:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: creating a model for second messenger system
Replies: 1
Views: 3852

Re: creating a model for second messenger system

I was wondering if someone has tried to model second messenger system (like one responsible for LTP generation showing cAMP kinetics) using NMODL I didn't realize that a model of LTP induction or expression involving cAMP had reached the "the" status. That aside, there have been lots of NEURON mode...
by ted
Sun Sep 11, 2005 11:31 am
Forum: Getting started
Topic: Somatic current injection
Replies: 1
Views: 4909

initialization

The default initialization in NEURON is a "global voltage clamp" initialization. That is, it sets the membrane potential throughout the entire model to v_init (whose numeric value appears next to the Init button), and forces all voltage- dependent variables to their steady state values for that memb...
by ted
Fri Sep 09, 2005 1:51 pm
Forum: Getting started
Topic: concentrations and reversal potential
Replies: 1
Views: 3449

ionic concentrations and equilibrium potentials

NEURON's default behavior is to treat equilibrium potentials as independent parameters, unless there is an ion accumulation mechanism that WRITEs the concentration of that particular ion. However, ion_style() allows you to change this behavior. Read about this here http://www.neuron.yale.edu/neuron/...
by ted
Fri Sep 09, 2005 10:58 am
Forum: Other questions
Topic: Total transmembrane current for segments
Replies: 5
Views: 6660

common pitfalls

Two pitfalls that everybody seems to run into, sooner or later:
1. Currents and conductances of distributed mechanisms have density units (i.e.
current/area and conductance/area).
2. The extracellular class's i_membrane contains ionic and capacitive current.
by ted
Fri Sep 09, 2005 10:54 am
Forum: Getting started
Topic: HH model with high positive current
Replies: 3
Views: 4600

temperature effects on squid axon excitability

As temperature increases, squid axon becomes less excitable, so a stronger stimulus
is needed to trigger a spike. To avoid gNa inactivation and gK activation, it is best to
increase stimulus strength by raising the amplitude of the stimulus, rather than
prolonging stimulus duration.
by ted
Fri Sep 09, 2005 10:50 am
Forum: Modeling networks
Topic: How to compile a self-defined integrate-fire MOD file?
Replies: 5
Views: 6841

load nrnmech.dll automatically

Under MSWin, when NEURON starts, it loads the nrnmech.dll file that it finds in thecurrent working directory, and prints the names of the mod files for any mechanisms that it finds in that nrnmech.dll. If you don't see such a message in NEURON's xterm window, then NEURON is not starting in the direc...
by ted
Fri Sep 09, 2005 10:28 am
Forum: Getting started
Topic: Hodgkin-Huxley parameters
Replies: 3
Views: 6399

OK, short answers. 1- which parameter define membranr resistance Ra? There is no membrane resistance parameter in NEURON. Ra isn't membrane resistance, it's cytoplasmic resistivity. Read the documentation. Start with the papers listed on the Documentation page at NEURON's web site. in toturial A , R...
by ted
Thu Sep 08, 2005 7:11 pm
Forum: Getting started
Topic: HH model with high positive current
Replies: 3
Views: 4600

Use the GUI for exploratory simulations

Good first step, but there are some things you might want to change-- A model with these anatomical and biophysical properties only needs nseg = 1. The time step is 0.1 microsecond, which is unnecessarily small. 0.025 ms would be perfectly adequate. Why wait 100 ms to apply the stimulus current? Now...
by ted
Thu Sep 08, 2005 6:52 pm
Forum: Hot tips
Topic: Exploit NEURON's GUI tools
Replies: 0
Views: 21952

Exploit NEURON's GUI tools

There seems to be a widespread assumption that "if you're not writing code, you're not doing real compuational modeling." Sometimes this manifests as snobbery against using NEURON's GUI, a kind of nerd-machismo that keeps people from taking advantage of the powerful tools that are available via the ...
by ted
Thu Sep 08, 2005 5:16 pm
Forum: Getting started
Topic: Help for the total beginner
Replies: 1
Views: 27873

Help for the total beginner

Go to NEURON's Documentation page
http://www.neuron.yale.edu/neuron/docs
and read "Help for the total beginner" under "Guides and Tutorials."
by ted
Thu Sep 08, 2005 11:35 am
Forum: Other questions
Topic: Square impulse stimulation.
Replies: 2
Views: 6643

square pulses, shmare pulses

Not to encourage or endorse religious debates about stimulus waveforms, I happen to be an electrical engineer, and count many EEs among my friends and acquaintances. I am unaware of any prejudice whatsoever, by anyone, against pulses of any shape. Why, where would textbooks on linear circuit theory ...