GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. 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.
Since its release for general use in 1988, GENESIS has provided one of the foundations for the ongoing course in Methods in Computational Neuroscience at Woods Hole MA, as well as courses offered in the European Union, Mexico, Brazil, India, and in more than 61 universities around the world, where it has been used both as an instructional tool in realistic modeling of the nervous system, and as a simulation based tool for neurobiological education in general. The most recent release of GENESIS, version 2.3, became available in March 2006, and runs under most UNIX-based systems with the X Window System, including Linux, OS/X and Windows with Cygwin. A major revision GENESIS 3 is currently under development.
We have spent considerable time and effort developing educational tutorials for instruction in both neurobiology and computational methods. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. For an example of the use of the GENESIS tutorials as the basis for a short unit on neural modeling, see the WWW version of some lectures given at the University of Colorado.
The 61 institutions of of which we are aware that have used GENESIS in instruction are:
* Arizona State University
* Autonomous University of Barcelona
* Boston University
* Brown University
* Caltech
* Case Western Reserve University
* Charles University (Prague)
* East Carolina University
* Emory University
* George Mason University
* Goettingen University
* Harvard University
* Harvey Mudd College
* Hiroshima International University
* Hong Kong University of Science and Technology
* Keele University (UK)
* King's College London
* Louisiana Tech University
* Massachusetts Institute of Technology
* McMaster University (Canada)
* Memorial University (St. John's NF)
* National Centre for Biological Sciences (India)
* Nencki Institute of Experimental Biology (Poland)
* Ohio University
* Oxford Brookes University (UK)
* Purdue University
* Rijksuniversiteit Groningen, Netherlands
* Royal University of Technology (Sweden)
* Stanford University
* Sunderland University
* Sussex University
* Syracuse University
* Technische Universitaet Dresden
* Texas A & M University
* Trinity College
* Trinity University
* United States Naval Academy
* Universidade de Sao Paulo
* Universidade do Rio Grande do Sul
* University of Aachen (Germany)
* University of Akron
* University of California at Los Angeles
* University of Chicago
* University of Colorado
* University of Connecticut Health Center
* University of Edinburgh (UK)
* University of Frankfurt
* University of Illinois at Urbana-Champagne
* University of Leipzig (Germany)
* University of Lubeck (Germany)
* University of Minnesota
* University of Missouri-Columbia
* University of Pittsburgh
* University of Quebec
* University of Southern California
* University of Texas (Dallas)
* University of Texas (Galveston)
* University of Texas (San Antonio)
* University of Texas Health Science Center (San Antonio)
* University of Toronto
* Yale University
GENESIS has formed the basis for the laboratory section of the Methods in Computational Neuroscience course (1988-1997) at the Marine Biological Laboratory, the Bangalore short course in Computational Neuroscience (1999-2000), and is used in the annual EU Advanced Course in Computational Neuroscience ( http://www.neuroinf.org/courses/EUCOURSE). It is also featured in the new Latin American School on Computational Neuroscience (2006, 2008) ( http://neuron.ffclrp.usp.br/lascon/home.htm). GENESIS was also used in a course directed and taught by the P.I. and sponsored by the National Academy of Sciences, in Mexico City in the summer of 1991. GENESIS tutorials have been given at the 2006 Frankfurt Institute of Advanced Study summer school on theoretical neuroscience and complex systems, at GENESIS Users Meetings (GUM), and in conjunction with the World Association of Modelers (WAM) Biologically Accurate Modeling Meeting (BAMM) in 2005 and 2006. The most recent versions of these tutorials have been included in the "Ultimate GENESIS Modeling Tutorial Distribution", a complete self-paced GENESIS modeling course that has been packaged for distribution on a CDROM, or installation on a hard drive.