NEURON vs GENESIS - Opinions, please?

Matt Jones jonesmat at physiology.wisc.edu
Sat Jun 29 20:49:10 EST 2002


mats_trash at hotmail.com (mat) wrote in message news:<43525ce3.0206260901.6c9f79 at posting.google.com>...

> 
> Also I think it would be useful to try and do the coding, may even
> give me greater understanding (!)
> 

I agree 100%. I learned an awful lot by writing my own simulator for a
small network of 3 HH neurons coupled by dynamic synapses (in Matlab).

The problem came when I wanted to -add- a neuron. I essentially had to
rewrite the code from scratch. This is probably the -main- advantage
of using a canned program. They've already implemented a built in
"scalability" (especially Genesis).

On the other hand, figuring out your own solution to the scalability
problem would sure teach you a lot too.


> Was thinking of using Matlab to analyse the data from the simulator
> (another way of saving on the amount I have to write compared to
> Neuron/Genesis which include custom analysis/graphic tools), is it
> relatively simple to integrate with other programs does anyone know? 

Yeah, Matlab is great. I use it for everything. It's very easy to
import data in text format, or standard image formats. If you need to
analyze something in a custom binary format, that's not too hard
either as long as you know the format exactly. I haven't -actually-
used it to analyze GENESIS output yet, but I would be shocked if there
was any problem doing that.

> I've read of the ability to compile Matlab analysis and graphing
> routines into standalone programs, has anyone any experience of this?

I've never done it, but i know there are some limitations. I don't
think the Matlab compiler handles the struct data type properly, and
there may be some issues with graphics too (because a lot of Matlab
graphics is object oriented, and probably relies on structs.

Another option with Matlab is that you can compile your own code, then
call that with Matlab. I find Matlab really great for writing GUIs, so
you could have a Matlab GUI front end for your simulator, the
simulator as compiled code, and a GUI backend for analyzing the
output. That would be efficient, because solving the diffeqs will be
the really cpu-intensive part so you would want that compiled. But you
may not want to write a whole GUI in fortran (can fortran even do a
gui?).


Oooh. This sounds like fun...


Cheers,

Matt



More information about the Neur-sci mailing list