GENESIS is a general purpose simulation platform which was
developed to support the simulation of neural systems ranging from complex
models of single neurons to simulations of large networks made up of more
abstract neuronal components. GENESIS has provided the basis for laboratory
courses in neural simulation at both Caltech and the Marine Biological
Laboratory in Woods Hole, MA, as well as several other institutions. Most
current GENESIS applications involve realistic simulations of biological
neural systems. Although the software can also model more abstract
networks, other simulators are more suitable for backpropagation and similar
connectionist modeling.
The current version of GENESIS and its graphical front-end XODUS are written
in C and run under UNIX on Sun (SunOS 4.x or Solaris 2.x), DECstation
(Ultrix), Silicon Graphics (Irix 4.0.1 and up) or x86 PC (Linux or FreeBSD)
machines with X-windows (versions X11R4, X11R5, and X11R6). Within the next
two months, we expect to complete the port of GENESIS to DEC Alphas (OSF1 v2
and v3), IBM RS6000s (AIX) and HPs (HPUX). Other platforms may be capable
of running GENESIS, but the software has not been tested by Caltech outside
of these environments.
The GENESIS ftp site also contains the first release of Parallel GENESIS,
designed for networks of workstations (NOW), symmetric multiprocessors
(SMP) and massively parallel processors (MPP). This release is known
to run on SGI/Irix and has run on these workstations: Sun4/Solaris,
Alpha/OSF1.3, DecStation/Ultrix4.3, Sun4/SunOS. It has run on these
SMPs: SGI-Challenge/Irix 5.3, Sun4MP/Solaris. It will soon be ported
to the Cray T3D/E MPP and later to Intel Paragon and IBM SP2 MPPs.
Improvements and New Features in GENESIS 2.0:
o rewritten source code provides a more portable, stable and consistent
system.
o revised command set and scripting language provides more consistent
command names and command options, and consistent syntax.
o script converter program translates GENESIS 1 scripts to GENESIS 2
o now runs on 486 and Pentium PC's under Linux and FreeBSD
o new treatment of synaptic connections eases the construction of network
models
o extended object facility allows the creation of new GENESIS objects at
the script level
o includes simulation scripts for all tutorials and examples used in ``The
Book of GENESIS''.
o completely revised and expanded manual and on-line help
o includes the first release of a parallel processing capability, allowing
a model to be partitioned and run on workstation clusters and on parallel
computers. Single simulations can be parallelized and automated
searches of parameter space can be performed in parallel.
o includes a suite of benchmarks ("Rallpacks") used for evaluating
GENESIS and other neural simulators for speed and accuracy.
The XODUS graphical interface has been completely rewritten featuring:
o independence from the Athena widget set, for increased portability and
a more attractive appearance
o greater interaction with simulations using the mouse (rescaling of
graphs by click and drag, restructuring of simulation elements with
drag and drop operations, etc.)
o new XODUS widgets and extended capabilities of existing ones allow
improved visualization of simulation results
Acquiring GENESIS via free FTP distribution:
We have made the current release of GENESIS (ver. 2.0, August 1995)
available via FTP from genesis.bbb.caltech.edu (131.215.5.249). The
distributed compressed tar file is about 3 MB in size. The current
distribution includes full source code and documentation for both GENESIS
and XODUS as well as fourteen tutorial simulations. Documentation for these
tutorials is included along with online GENESIS help files and postscript
files for generating the newly revised printed manual.
To acquire the software use 'ftp' to connect to genesis.bbb.caltech.edu and
login as the user "anonymous", giving your full email address as the
password. You can then 'cd /pub/genesis' and download the software. Be
sure to download the files LATEST.NEWS and README for information about new
features of the current GENESIS version, the files on the system, and
installation instructions.
A detailed guide to the GENESIS neuroscience tutorials and to the
construction of GENESIS simulations is given in:
The Book of GENESIS: Exploring Realistic Neural Models with the GEneral
NEural SImulation System, by James M. Bower and David Beeman, published by
TELOS/Springer-Verlag -- ISBN 0-387-94019-7
For ordering information, contact info@telospub.com, or phone (in the US)
1-800-777-4643.
BABEL - GENESIS users group
Serious users of GENESIS are advised to join the users group, BABEL.
Members of BABEL are entitled to access the BABEL directories and email
newsgroup. These are used as a repository for the latest contributions by
GENESIS users and developers. These include new simulations, libraries of
cells and channels, additional simulator components, new documentation and
tutorials, bug reports and fixes, and the posting of questions and hints for
setting up GENESIS simulations. As the results of GENESIS research
simulations are published, many of these simulations are being made
available through BABEL. New developments are announced in a newsletter
which is sent by email to all members. Members are able to access the BABEL
directories and transfer files to and from their host machines using a
passworded ftp account.
Inquiries concerning GENESIS should be addressed to
genesis@bbb.caltech.edu. Inquiries concerning BABEL memberships should be
sent to babel@bbb.caltech.edu. Other information concerning GENESIS,
including "snapshots" of GENESIS simulations and descriptions of research
which has been conducted with GENESIS may be found on the GENESIS World Wide
Web Server: http://www.bbb.caltech.edu/GENESIS
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Prof. David Beeman, GENESIS Users Group - dbeeman@dogstar.colorado.edu
GENESIS WWW site - http://www.bbb.caltech.edu/GENESIS
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