neural net software

Michael Hucka hucka at eecs.umich.edu
Sun Feb 9 23:45:29 EST 1997


>>>>> On 09 Feb 1997, KAJ at gnn.com (Kenneth Jenrow) wrote:

  KAJ> I am requesting that anyone with some experience with presently
  KAJ> available neural network software packages please provide reviews of
  KAJ> each. Alternatively, if there is a single package which dominates
  KAJ> please provide information about it.  I am primarily interested in
  KAJ> modelling hippocampal and neocortical networks. Thanks to all who
  KAJ> respond.

Whenever you ask for information about any software, please remember to tell
people what kind of computer platform you're using, whether it's a UNIX
workstation, or a PC, or a Mac, or something else.

I have only minor experience with the following, so I can't provide actual
reviews, but in case you don't get any other information, here's a summary of
a few major packages.  A longer list of general neural network software and
additional tips and information can be found in the comp.ai.neural-nets FAQ
(frequently-asked questions) list, available from
ftp://ftp.sas.com/pub/neural/FAQ.html.  The items below are free software
specifically geared towards biologically-motivated simulations.

GENESIS 2.0.2
    A general-purpose neural simulation system.  It is useful for a range of
    types of simulations, from detailed simulations of parts of single
    neurons, to large networks of many abstract neurons.  It is used in the
    computational neuroscience course offered at the Marine Biological
    Laboratory at Woods Hole, MA.

    Platforms: UNIX + X Windows
    More info: http://www.bbb.caltech.edu/GENESIS/.

NEURON 3.2.2
    Another general-purpose simulation system, providing somewhat more
    elaborate features (IMHO) in the area of detailed neural simulation than
    GENESIS.  Like GENESIS, this has been used at the MBL computational
    neuroscience course.

    Platforms: UNIX + X Windows, NeXT, 486PC's with Linux or MS Windows
    More info: ftp://ftp.nnc.yale.edu/neuron/

BIOSIM
    A biologically-oriented neural network simulator.  From the README file:
    "Four neuron models are implemented: a simple model only switching ion
    channels on and off, the Hodgkin-Huxley model, the SWIM model and the
    Golowasch-Buchholz model as the most enhanced model.  Dendrites consist
    of a chain of segments without bifurcation.  A neural network can be
    created by using the interactive network editor which is part of
    BIOSIM. Parameters could be changed via context sensitive menus and the
    results of the simulation can be visualized in observation windows for
    neurons and synapses.  Stochastic processes such as noise can be
    included.  In addition, biologically orientied learning and forgetting
    processes are modeled, e.g. sensitization, habituation, conditioning,
    hebbian learning and competitive learning.  Three synaptic types are
    predefined (an excitatatory synapse type, an inhibitory synapse type and
    an electrical synapse).  Additional synaptic types can be created
    interactively as much as desired."

    Platforms: UNIX + X Windows
    More info: ftp://ftp.uni-kl.de/pub/bio/neurobio/biosim.readme

Many other packages exist that are better-suited to simulating abstract
networks of the back-propagation or self-organizing map variety.  Again, the
comp.ai.neural-nets FAQ has a good list of these.

-- 
Mike Hucka    hucka at umich.edu    http://www.eecs.umich.edu/~hucka    University
 PhD to be, computational models of human visual processing (AI Lab)     of
   UNIX systems administrator & programmer/analyst (EECS DCO)         Michigan



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