BIOSIM - Biol. NN-Simulator

Stefan Bergdoll bergdoll at zxd.basf-ag.de
Wed Dec 8 06:05:37 EST 1993


                      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

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