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Neural Simulation Software

Michael Ferber Ferber at zoology.uni-frankfurt.de
Sun Jan 28 05:18:34 EST 1996

In article <4epk8o$35i at mozz.unh.edu>,
   eet at kepler.unh.edu (Eric E Thomson) wrote:
>	I am interested in obtaining software that allows you to simulate 
>_simple_ neural circuits (to be used as a pedagogical tool in intro 
>neurobiology courses).  I want something that a neurologist would find 
>useful, perhaps something which lets you form simple excitatory and 
>inhibitory feedbacks among cartoon neurons.  I am interested in neural 
>networks, but only insofar as they get across the way neurons and groups 
>of neurons might  actually work (and it should be in a way that can be 
>presented to a class of undergrads on an overhead screen).  
>	I would appreciate any information about such programs (on the 
>Mac or the PC).

I think the software package biosim, which was developed at the university of 
Kaiserslautern may be the right one for you. I di not know a WWW link, but you 
can FTP it from:

ft.uni-kl.de in the directory /pub/bio/neurobio

There are versions for DOS and UNIX. Here some more info.


$$$ This package is NOT the BIOSIM program of Per Hammarlund (Sweden) !!!!  

Date: 8 Dec 1993 11:05:37 GMT
Newsgroups: bionet.software
Subject: BIOSIM - Biol. NN-Simulator


                      BIOSIM - Biol. NN-Simulator

       BIOSIM is a biologically oriented neural network simulator.

* It's public domain.
* It runs on Unix (a less powerful PC-version is available, too).
* It's easy to install.
* It's bilingual (german and english)
* It has a GUI (Graphical User Interface).
* It doesn't requires to learn a simulation language.
* It was designed for research and teaching.
* It includes learning capabilities.
* It provides online help facilities.
* It offers controlling interfaces.
* A batch version is available.
* A DEMO is provided, covering a wide range of application features.


ftp ftp.uni-kl.de (or ftp
login in as "ftp" (or "anonymous"), give your email address as a password

cd /pub/bio/neurobio
mget biosim.readme biosim.tar.Z
mget readme.txt biosimpc.zip (only needed if the PC-version is required)

REQUIREMENTS (for the Unix version)

- Unix workstation with X11 Rel. 3 and above, Motif Rel 1.0 and above
- At least 12 MB of physically memory, recommended are 24 MB and more
- 20 MB disc space
- A C-compiler (the GNU C-compiler gcc is recommended)

REQUIREMENTS (for the PC version)

- PC or PC-compatible  with MS Windows 3.0 and above
- At least 4 MB of physically memory, recommended are 8 MB and more
- 1 MB disc space


Four neuron models are implemented in BIOSIM: a simple model only
switching ion channels on and off, the original Hodgkin-Huxley model,
the SWIM model (a modified HH 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 can 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
A demonstration shell script, which controls the simulator, is
included showing a wide range of possibilities with BIOSIM.
Within BIOSIM a handbook and an online-help system is available.
BIOSIM is bilingual (english and german). When installing BIOSIM the
user can choose between english and german. Thus, a english or german
environment is installed. The INSTALL procedured is bilingual, too.
The biological and mathematical model underlying BIOSIM were
developed by Dr. Uwe T. Koch (university of Kaiserslautern, Germany)
and Stefan Bergdoll (BASF Inc., Germany).
The BIOSIM simulator, as well as the online help system, were
developed by Stefan Bergdoll (BASF Inc., Germany).

Stefan Bergdoll
Department of Software Engineering (ZXA/US)
D-67056 Ludwigshafen, Germany

bergdoll at zxa.basf-ag.de
tel 0621-60-21372
fax 0621-60-43735

Hope this helps


|| Dr. Michael Ferber                     ||
|| Universitaet Frankfurt                 ||"science moves,
|| Zoologisches Institut                  || but slowly, slowly ......"
|| email: Ferber at zoology.uni-frankfurt.de ||                      Tennyson

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