Large scale biologically realistic simulations.

[Per Hammarlund]

Hello,

I have a question concerning implementations of programs for
biologically realistic simulations on massively parallel machines or
other "super" computers. In fact, what I am most interested in is
whether anyone has, or knows of, simulations software (for any
computer) that is capable of simulating something like 50,000 neurons
and in the order of 1,000,000 synapses.

I am interested in these programs as we have implemented a program on
the Connection Machine, from Thinking Machines Corp, that can do about
that, on the 8k machine we have at KTH. The title and abstract of the
preliminary report (TeX syntax, please ignore) is enclosed below.

Pointers to reports are greatly appriciated!

Thank you very much!

Per Hammarlund
SANS-NADA
KTH, Royal Inst. of Tech.
S-100 44 Stockholm
Sweden

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				biosim
		 A Program for Biologically Realistic
		  Neural Network Simulations on the
			  Connection Machine

		   Bj\"orn Levin and Per Hammarlund
		 Studies of Artificial Neural Systems
	Department of Numerical Analysis and Computer Science}
				   
			    TRITA-NA-P9021

This paper describes a program for biologically realistic neural
network simulations on the Connection Machine. The biosim program
works as a back end to another program, swim, that handles the user
interaction and specification of the neural network. The swim program
takes a specification of the neural network and generates a parameter
file that is read into the biosim program and processed. The output
has the same format as the output of the swim program. The purpose of
the biosim program is to make simulations of larger networks possible.

The neuron model that is used in the simulations is a
compartmentalized abstraction of the neuron. One of the compartments
acts as the soma, ie the cell body, and the rest act as parts of the
dendrite tree. The voltage dependent ion channels are modeled using
Hodgkin-Huxley-like equations.  The program supports Na+, K+, Ca2+,
and Calcium dependent K+ channels.  Synaptic interaction includes the
voltage gated NMDA receptors and conventional kainate/AMPA receptors.
Hooks provided in the code make the addition of new types of channels
and receptors extremely easy.

The program is capable of handling some tens of thousands of
compartments and about ten times that number of synapses on an 8K
machine. The numerical method used in solving the differential
equations is aimed at speed at the expense of some accuracy.

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