The GENESIS 2 simulator home page

http://genesis-sim.org/GENESIS is the home page
for the stable, "classic" GENESIS 2 simulator.

After the "final" release of of GENESIS 2.3 in March 2006, development efforts shifted towards GENESIS 3 (G-3), a 21st century neural simulator without the limitations of GENESIS 2 and other simulators that were developed in the late 1980's and 90's. At this point, G-3 is still in the development stage.

The main home page for the GENESIS simulator is at http://genesis-sim.org. It is devoted primarily to G-3 and serves as the repository for downloads and updates of the G-3 Developers Release. It also supports the GENESIS Documentation System, and has many resources for users of GENESIS 2. Be sure to click on the tabs for Documentation, Models, Libraries, and Education for recent GENESIS 2 documentation and user contributed materials.

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 Sourceforge genesis-sim-users mailing list is the best means of obtaining individualized help with GENESIS 2 or 3. You may subscribe at https://lists.sourceforge.net/lists/listinfo/genesis-sim-users.

This page at http://genesis-sim.org/GENESIS contains links to older GENESIS 2 material, as well as some recently added material. Most of this is also accessible via links from the main genesis-sim.org page.

Recent GENESIS 2 developments

Although GENESIS 2 is user-suported, rather than being being actively developed, users continue to contribute new libraries, documentation, and simulation scripts. Questions posted to the genesis-sim-users mailing list usually receive a prompt response. GENESIS 2.3 continues to be widely used used for large network models consisting of multicompartmental neurons, and for projects in modeling courses, such as the recent Latin American School on Computational Neuroscience (LASCON V).

Although GENESIS 2.3 was intended to be a final release of the GENESIS 2 series, it has continued to evolve, with modifications needed to efficiently implement synaptic plasticity in large networks and many contributions from users. This has made it necessary for a new November 2014 GENESIS 2.4 release.

This new release is now avalable for download at
http://genesis-sim.org/GENESIS/genesis-ftp/genesis-2.4-src.tar.gz.

The GENESIS 2.4 release includes:

The revised "Ultimate GENESIS Tutorial Distribution" was used as course materials for the tutorial Constructing biologically realistic neuron and network models with GENESIS on July 26th at CNS 2014, presented by Hugo Cornelis.

You can download it as:

UGTD2-CNS.tar.gz or UGTD2-CNS.zip

More information about the "UGTD" is below.

Some recently added GENESIS 2 tutorials and simulations

Ultimate GENESIS Tutorial Distribution

This is a complete self-paced GENESIS modeling course, combined with GENESIS binary and source distributions and installation instructions. It provides an easy way to get everything by downloading a single package. The latest version may be browsed from this link.

VAnet2 - An efficient hsolved GENESIS version of the Vogels and Abbott (2005) model that was used in the Brette et al. (2007) review of network simulators. It serves as a tutorial on the use of hsolve with network models in order to achieve speedups by a factor of 10 to 20. The 'VAnet2-batch.g' script is intended to be extended for testing GENESIS spike timing dependent plasticity (STDP) implementations with hsolve. This script would be a good starting point for models that use more realistic cells and connections.

ACnet2 - An auditory cortex model that also serves as a tutorial and template for creating neocortical network models.

fMRInet Is a variation of the ACnet2 model that illusrates how to provide unusual stimuli, such as the effects of the electromagnetic fields that are produced during an fMRI experiment. This is done by using a 'script_out' object to provide the stimulus at clocked intervals.



Older GENESIS News and Links



What is GENESIS? Learn more about GENESIS here


GENESIS and PGENESIS 2.3 ARE NOW AVAILABLE!

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.

Announcing the Sourceforge GENESIS development site

http://sourceforge.net/projects/genesis-sim

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.

Plans for GENESIS 3

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.

Summary of recent GENESIS developments


GENESIS Downloads

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.


GENESIS Tutorials and Documentation

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.


BABEL

The GENESIS Users Group


What is BABEL?

How to join the GENESIS Users Group, BABEL

Coming soon:

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 Users Meetings

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.


Other GENESIS Resources and Links

Bug Fixes

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).


If you have any questions regarding GENESIS, please email: genesis@genesis-sim.org

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.


The GENESIS web site was established June 30, 1994.