Search found 5729 matches

by ted
Sun Sep 04, 2005 1:37 pm
Forum: Hot tips
Topic: GUI tools: Shape Name
Replies: 0
Views: 4489

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: 10490

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: 11443

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...
by ted
Sat Sep 03, 2005 8:03 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: programatically changing the temperature
Replies: 8
Views: 11443

Re: programatically changing the temperature

That was a clever approach, and I can see how there's no way that one could tell in advance that it wouldn't work. It's actually much easier to change any parameter in the course of a simulation. This code will drive celsius in a linear ramp from 6.3 to 20 deg C over the course of 100 ms (pretty fas...
by ted
Sat Sep 03, 2005 6:05 pm
Forum: Getting started
Topic: VClamp and IClamp in the same .hoc file
Replies: 4
Views: 8269

diagnosing "object prefix is NULL"

all I get is a 'record : object prefix is NULL' error message Is vec[2] already a Vector before you assert .record()? To find out, insert print vec[2] before the vec[2].record(&vstim.i,1) statement An aside to help you avoid future pain: I have tried to record it into a vector with something like v...
by ted
Fri Sep 02, 2005 10:46 am
Forum: Getting started
Topic: units
Replies: 1
Views: 3743

Units

Excellent question. The first place to look: 1. Go to NEURON's home page http://www.neuron.yale.edu/ 2. Click on the Documentation link 3. On the Documentation page, click on the FAQ link 4. On the FAQ page find the link What units does NEURON use for current, concentration, etc.? For more informati...
by ted
Thu Sep 01, 2005 11:08 am
Forum: Other questions
Topic: Working with strings
Replies: 3
Views: 5417

use StringFunctions to manipulate strings

Use the StringFunctions class to work with strings--see http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/classes/strfun.html "Imagine an alternate universe in which all life forms are computer programs. What controversy would result if a copy of NEURON fell into the hands of local p...
by ted
Wed Aug 31, 2005 12:56 pm
Forum: Anatomically detailed models
Topic: Reducing complex models to equivalent cables
Replies: 9
Views: 10725

Re: attenuation

1) I assume that imp.ratio(freq) is the attenuation value we need to calculate L = log(A), correct? It's the voltage transfer ratio, defined as "voltage downstream/voltage upstream", which is necessarily <= 1. Attenuation, however, is the inverse of this. You will find the Impedance class described...
by ted
Wed Aug 31, 2005 11:59 am
Forum: Getting started
Topic: VClamp and IClamp in the same .hoc file
Replies: 4
Views: 8269

Re: VClamp and IClamp in the same .hoc file

I have a model neuron with several conductances, and I want to test its behavior with both v-clamp and i-clamp experiments (not at the same time, of course). My .hoc file defines the procedures 'dovc' and 'doic', which perform several pulses of either voltage or current clamp and plot the results i...
by ted
Tue Aug 30, 2005 6:01 pm
Forum: Other questions
Topic: how to print a model neuron with diameter information
Replies: 3
Views: 4292

Re: how to print a model neuron with diameter information

Another interpretation of your question is "how do I print a picture of the cell that shows how diameter changes along each section." Many of NEURON's GUI tools include a Shape plot that displays a projection of the cell onto the xy plane. By default, Shape plots show just the centroid of each secti...
by ted
Mon Aug 29, 2005 11:31 am
Forum: Modeling networks
Topic: Hf Stimulus Network Performance: Event Delivery or Pointers?
Replies: 10
Views: 11410

event delivery without adaptive integration

Given the high frequency stimulation regime every instance of cvode is thrown back to an extremely small dt once every ms. It is this interaction of event delivery and cvode which might make the high frequency stimulation regime an exception to the rule. It isn't the event delivery system itself th...
by ted
Sun Aug 28, 2005 11:54 am
Forum: Getting started
Topic: rebound spike
Replies: 1
Views: 5178

Creating, debugging, and tuning a model

i create a soma that include passive channel+HH channel and CaT channel. What do you mean by "HH channel? There is no such thing as an "HH channel." There is an "HH model of the action potential," which consists of three ionic currents: voltage-gated sodium and potassium currents, and a leak curren...
by ted
Thu Aug 25, 2005 1:19 pm
Forum: Getting started
Topic: HH channel and negative inject current
Replies: 1
Views: 4139

rebound spike, or anode break excitation

Without playing with the model you mention, my guess is that you are seeing something that is called rebound spiking, or anode break excitation. This is an interesting property of many kinds of excitable tissue, and you will find it described and explained in standard neuroscience textbooks. You mig...
by ted
Thu Aug 25, 2005 1:10 pm
Forum: Modeling networks
Topic: Hf Stimulus Network Performance: Event Delivery or Pointers?
Replies: 10
Views: 11410

event delivery system vs. pointers for synaptic connectivity

The price to pay for moving to pointers could be huge. One thing we know for sure: the overhead for numerical integration is a lot more than the overhed of the event delivery system. If you need to be convinced, compare run times for a net of integrate and fire cells vs. a net with the same archite...