Sheet of neurons simulation

Larry Hunter hunter at work.nlm.nih.gov
Thu Feb 18 17:48:18 EST 1993

Francis Burton asks:

  On behalf of a colleague, I am looking for software that can be used to
  simulate large networks of connected neurons.

Well, there are many public domain (or nearly so) neural network simulators
out there that can do arbitrary topologies and update rules, at least with a
little bit of programming.  IMHO, by far the best, both in terms of what
comes with the system and how easy it is to program to meet specific needs,
is the Xerion system from University of Toronto.  It has wonderful graphical
interfaces (X windows) and runs on practically any Unix/X platform.  It is
originally designed for use in machine learning and on artificial neural
nets, but I think it offers a good possibility for adaptation to natural
neural network simulation.  Also, the author of the program, Drew van Camp
is pretty accessible.

It is available by anonymous ftp from the host ai.toronto.edu in the
directory /pub/xerion.

Here's a snippet from the README file:

  Xerion is a Neural Network simulator developed and used by the
  connectionist group at the University of Toronto. It contains libraries of
  routines for building networks, and graphically displaying them.  As well
  it contains an optimization package which can train nets using several
  different methods including conjugate gradient. It is written in C and
  uses the X window system to do the graphics. It is being given away free
  of charge to Canadian industry and researchers. It comes with NO warranty.

  This distribution contains all the libraries used to build the simulators
  as well as several simulators built using them (Back Propagation,
  Recurrent Back Propagation, Boltzmann Machine, Mean Field Theory, Free
  Energy Manipulation, Kohonnen Net, Hard and Soft Competitive Learning).
  Also included are some sample networks built for the individual

  There are man pages for the simulators themselves and for many of the C
  language routines in the libraries. As well, xerion has online help
  available once the simulators are started. There is a tutorial on using
  Xerion in the 'doc' directory.

I hope this does what you want.


Lawrence Hunter, PhD.
National Library of Medicine
Bldg. 38A, MS-54
Bethesda. MD 20894 USA
tel: +1 (301) 496-9300
fax: +1 (301) 496-0673 
internet: hunter at nlm.nih.gov
encryption: PGP 2.1 public key via "finger hunter at work.nlm.nih.gov"

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