Search found 97 matches

by neuromau
Tue Oct 12, 2010 2:58 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7455

Re: Using ions in multiple mechanisms

Without the TABLE lines, the discrepancy increases. I guess that I can't make analogous changes to what was done in the other post ( http://www.neuron.yale.edu/phpBB/viewtopic.php?f=15&t=1246&start=0 ), probably because the inf and tau expressions in the hyperde3 mechanism are not exactly of the for...
by neuromau
Fri Oct 08, 2010 9:46 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7455

Re: Using ions in multiple mechanisms

Will the revised code find its way into ModelDB? Future users would find that to be a great benefit. Absolutely! My time investment, especially in the time taken for documentation, is really only worth it if I share the product with others. I've gotten through most of the code, rewriting, comparing...
by neuromau
Tue Oct 05, 2010 1:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7455

Re: Using ions in multiple mechanisms

For the sake of completeness: I also realized how it was possible that the mechanism contained currents for both the control and the treated model, without applying both currents to each model: Ex: hyperde3.mod (HCN channel) uses the following ions: hyf, hys, hyhtf, hyhts (the other thing that I fin...
by neuromau
Tue Oct 05, 2010 11:20 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7455

Re: Using ions in multiple mechanisms

In this case, it might make sense to define a new ion for the Ca channels that affect the Ca-gated K channels, so it can have its own accumulation mechanism. Yes, they also have many different Ca2+ ions, and as there are some Ca2+ dependent K+ channels, your note likely explains the multiple Ca2+ i...
by neuromau
Tue Oct 05, 2010 12:36 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7455

Using ions in multiple mechanisms

Hello, I have a few questions about using ions in mechanisms. I was looking through the mechanisms in ModelDB #124513 http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=124513 (Santhakumar/Morgan dentate gyrus model). I also emailed the programmers my question, but wanted to get other general ...
by neuromau
Sat Oct 02, 2010 6:52 pm
Forum: The GUI
Topic: Specify which cells get plotted in a Shapeplot?
Replies: 4
Views: 6301

Re: Specify which cells get plotted in a Shapeplot?

Perfect, thanks!
by neuromau
Fri Oct 01, 2010 9:12 pm
Forum: The GUI
Topic: Specify which cells get plotted in a Shapeplot?
Replies: 4
Views: 6301

Specify which cells get plotted in a Shapeplot?

Hello, I wrote some hoc code that defines 4 unique cells with positions such that they are arranged in a row when I create a Shapeplot. Now I am wondering if I can limit which cells are displayed in a Shapeplot, ideally making a separate Shapeplot for each cell? I'm fine with a solution using hoc, i...
by neuromau
Thu Sep 23, 2010 5:40 pm
Forum: Suggestions and Feedback
Topic: Typo in reference
Replies: 3
Views: 15138

Re: Typo in reference

Something happened to the text in this documentation page: http://www.neuron.yale.edu/neuron/static/docs/refman/obj.html . The last section 'Footnotes; Inheritance and Polymorphism' has a few incomplete sentences that don't seem to directly follow each other: ... A language supports Polymorphism whe...
by neuromau
Thu Sep 16, 2010 2:42 am
Forum: NEURON Announcements
Topic: The NEURON Book: errata and discussion
Replies: 37
Views: 55420

for (var) stmt example

What about this? P. 114, section 5.6.4: Working with range variables. It gives an example for iterating over each node including 0 and 1, and then a 'variant' that excludes 0 and 1, but the variant is the same as the original syntax:

Code: Select all

for (var) stmt
Thanks,
Marianne
by neuromau
Fri Sep 03, 2010 8:27 pm
Forum: Suggestions and Feedback
Topic: Compile under Linux - Other options
Replies: 1
Views: 11212

Compile under Linux - Other options

Hello, I was looking at the 'Compiling NEURON under UNIX/Linux page: http://www.neuron.yale.edu/neuron/download/compile_linux . In the Other Options section, I noticed it doesn't mention compiling with paranrn for parallel NEURON. Though the instructions for paranrn can be found here, http://www.neu...
by neuromau
Fri Sep 03, 2010 8:24 pm
Forum: Getting started
Topic: Course: Using ModelDB Mainen and Sejnowski 1996
Replies: 6
Views: 2119

Re: Course: Using ModelDB Mainen and Sejnowski 1996

The Mainen and Sejinowski, 1996 model has an Na (sodium channel) mechanism, as you can see from looking at the files in that modeldb entry (there is a file called "na.mod"). So that line is for inserting the sodium channel mechanism defined in "na.mod" into all the sections.
by neuromau
Mon May 10, 2010 8:58 pm
Forum: Parallel NEURON
Topic: Error with pc.allreduce
Replies: 2
Views: 2571

Re: Error with pc.allreduce

Thanks! Now that I have my arguments in the correct order, it works just fine =).
by neuromau
Wed May 05, 2010 10:35 pm
Forum: Parallel NEURON
Topic: Error with pc.allreduce
Replies: 2
Views: 2571

Error with pc.allreduce

Hello, I have an issue using pc.allreduce. I'm running code in parallel on my '2-core' Windows Vista machine using Neuron 7.2 installed at the Parallelization Course. Previously, this code worked fine with the following calls for 1 or 2 processors: mpiexec -n 1 /mypath/nrniv -mpi mycode.hoc mpiexec ...
by neuromau
Mon Aug 24, 2009 6:51 pm
Forum: Parallel NEURON
Topic: Access attribute of object owned by other host
Replies: 3
Views: 1810

Re: Access attribute of object owned by other host

Are the xyz coords empirical data or can they be generated algorithmically by any host that wants them and knows the gid of the cell? . The latter - algorithmically. Each host made its own copy of the position vector and just looked up any cell's position as necessary. Right now I'm working with a ...
by neuromau
Mon Aug 24, 2009 3:47 pm
Forum: Suggestions and Feedback
Topic: Typo in reference
Replies: 3
Views: 15138

Typo in reference

Hi, I just noticed this typo in the programmer's reference and wasn't sure where to post for it:
The SYNTAX for Entry "x3d" reads "x3d" but it should read "x3d(i)".

Thanks,
Marianne