🚀 go-pugleaf

In article <3ea7bl$fga@portal.gmu.edu>, herwin@osf1.gmu.edu (HARRY R. ERWIN) writes:
|> Interim Report/Lessons Learned on a Simulation Model of the Olfactory Bulb
|> 
|> Harry Erwin
|> January 1, 1995
|> 
|> As a graduate school project during the last quarter, I've been developing
|> a computational and compartmental model of a small but biologically
|> realistic subset of the olfactory bulb. It owes its primary inspiration to
|> the work done by Walter Freeman and James Skinner, but its many errors
|> naturally remain the responsibility of the author. 
|> 
|> I'm posting this report for anyone who might provide useful critical
|> feedback. The simulation consists of a number of small compartmental
|> models of sensory, tufted/mitral, periglomerular, and granule cell neurons
|> structured to provide insight into architectural details of the olfactory
|> bulb. Crucial omissions include reafference from the anterior olfactory
|> nucleus, the pyriform cortex, and the locus coeruleus and the effect of
|> changes in the chloride gradiant in the glomeruli. 
|> 
|> The model is written in C++ and represents 32 tufted/mitral cells and the
|> associated periglomerular and granule cells. The code is efficient, and
|> performance is excellent, both on a Macintosh IIfx and on a Silicon
|> Graphics Iris Workstation. On the SGI, approximately 200 milliseconds of
|> activity is modeled in 8 minutes of CPU time. The model has been rehosted
|> on PVM 3 and will eventually be moved to the Paragon supercomputer. 

Why are you writing your own simulator rather than using, for example,
NEURON, written by Michael Hines? This simulator has been refined over
several years and solves many of the problems encountered when writing
your own. It uses very fast and efficient numerical integration routines;
My model of 100 9-compartment cortical neurons connected at a density of
10% simulates 500 ms in 9 minutes of CPU time on a MIPS 3000. Its
modular nature allows the easy addition of arbitrary processes such
as the graded/electical synapses you mention. It has an Interviews front
end for graphical display, control and online modification of the
simulation.

To produce a simulator as good as NEURON you would need to spend
several years programming and testing - that time would be better spent
doing the actual simulations. In addition users of NEURON share their
simulation code, giving you access to many types of ion channels, synapses
etc.

You can ftp NEURON from neuron.neuro.duke.edu.

Paul