The new web site has improved forums (replacing those on the Sourceforge site) that allow users to attach files to postings. It also provides the ability for GENESIS users to add new content such as simulations, documentation, and tutorials. The genesis-sim.org forums and the Sourceforge genesis-sim-users mailing list are the best means of obtaining individualized help with GENESIS.
This older site at http://genesis-sim.org/GENESIS is no longer being maintained, but contains files that may not yet be accessible from the new home page. Please be aware that newer versions of some of this material may be available from the main GENESIS site.
GENESIS and PGENESIS 2.3 ARE NOW
GENESIS 2.3 supercedes version 2.2.1, and has a number of changes in the simulator source code to allow use on a greater variety of platforms, including Intel and AMD 64 bit processors, MacIntosh with OS/X, and Microsoft Windows with the Cygwin environment. It includes Kinetikit Version 11, Version 2 of the Purkinje cell tutorial, some new objects and enhancements of existing ones, plus revised and updated documentation. For more details of the new features in GENESIS 2.3, see the section on Changes Introduced in GENESIS 2.3 in the GENESIS 2.3 Reference Manual.
PGENESIS 2.3 now has support for MPI as well as PVM. It should run on almost any parallel cluster, SMP, supercomputer, or network of workstations where MPI and/or PVM is supported, and on which serial GENESIS itself is runnable. There have been many updates to the documentation for this new version.
We expect that GENESIS 2.3 will be the last GENESIS 2 release, before we begin preliminary releases of GENESIS 3. Therefore we encourage all GENESIS users to upgrade to this (hopefully) final GENESIS 2 release. Please see the GENESIS Downloads section below.
This contains the CVS Repository for the latest GENESIS development versions, as well as public forums for reporting bugs or compiling problems, and for discussing issues related to GENESIS development.
We are developing a completely new version of GENESIS, to have a modular architecture with plugins and multiple interfaces. This will allow the use of multiple simulation engines such as MOOSE (http://moose.sourceforge.net/) or Neurospaces (http://www.neurospaces.org/). In addition to greater simulation speed, this will offer greatly improved capabilities of interfacing GENESIS 3 with external programs, other simulation environments, web-based applications, and visualization tools. Read about our plans for GENESIS 3 here.
Download the GENESIS and PGENESIS distributions
The final (March 2006) releases of GENESIS and PGENESIS version 2.3 are now available for download. In addition to the full GENESIS distribution with source code, precompiled binary versions for Linux and Windows with Cygwin are also available. The binary versions for Mac OS/X are now available to download from the the Sourceforge GENESIS development site http://sourceforge.net/projects/genesis-sim.
Use this link to browse the GENESIS archive and download the newest release of GENESIS, PGENESIS, and more. Be sure to read the README file for the GENESIS archive. This contains a description of new features in the latest versions of GENESIS and Parallel GENESIS (PGENESIS), and will allow you to determine which files to download.
Summary of available GENESIS Tutorial Simulations
Hypertext version of the GENESIS 2.3 Reference Manual
Download the manual: Hyperdoc.tar.gz
The Book of GENESIS (A guide to neural modeling with GENESIS.)
Book of GENESIS - Downloadable Internet Edition
The Book of GENESIS, originally published as a Springer-Verlag imprint, is now out of print. As the publisher does not plan to reprint the book, the copyright has been reclaimed by the authors, and we are now able to offer it to be downloaded from the internet at no cost.
What is BABEL?
How to join the GENESIS Users Group, BABEL
The existing BABEL web site (http://www.genesis-sim.org/BABEL) with its libraries of GENESIS simulations and other material is being incorporated into a new GENESIS site, which will be announced soon.
The updated collection of user-contributed material from BABEL, including the archive of GENESIS models, is available here.
New features on the way are:
GENESIS developmemt now involves contributions from many users and developers from outside the Bower laboratory. Therefore we have recently had a yearly GENESIS Users Meeting (GUM) to bring together GENESIS users and developers to discuss user needs and developer priorities. The 2005 meeting was held March 31 - April 2 in conjunction with the World Association of Modelers (WAM) First Annual Biologically Accurate Modeling Meeting (BAMM).
This meeting combined a day of tutorials on realistic neural modeling techniques followed by two days of scientific presentations. The meeting's overall objective is to promote communication and collaboration between users and others involved in realistic biological modeling and to provide an introduction to other interested scientists. Because of the enthusiastic response to this meeting, it was repeated again as WAM-BAMM*06, held March 22 - 25, 2006. In addition to tutorials and scientific presentations, the 2006 meeting included a workshop and open discussion on GENESIS 3 development issues. The next GUM will be held in 2008. Details will be announced on the GENESIS site and through the GENESIS users mailing list.
If you experience any trouble installing or running GENESIS, be sure to check the forums at the main site for GENESIS 2 development, http://sourceforge.net/projects/genesis-sim. The CVS repository at this site will be kept up-to-date with the most recent bug fixes. The Bug-fixes directory at the GENESIS ftp site, currently contains fixes for older versions of GENESIS. If there are significant fixes for GENESIS 2.3, they will also be added. The README file and the file compiling.problems describe any patches or changes that have been added, and provide hints on solving common compilation problems.
Use of GENESIS in Research
Recent publications involving GENESIS
Use of GENESIS in Education
GENESIS on Parallel Computers
Information on the
GENESIS-based Neural Database and Modeler's Workspace
(part of the Human Brain Project).
Please note the new addresses for GENESIS email and the GENESIS web page. If you have been directed here from the old Caltech GENESIS site, please update your bookmarks and address books.