What is GENESIS?


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 GENESIS applications involve realistic simulations of biological neural systems. Currently GENESIS and the parallel version PGENESIS are used on parallel supercomputers to simulate cortical networks that contain millions of mult-compartmental neurons. Although the software can also model more abstract networks, there exist other simulation packages that are more suitable for networks of point integrate-and-fire neurons, or connectionist modeling.

Since its release for general use in 1988, GENESIS has provided one of the foundations for neural modeling courses, begining with the course on Methods in Computational Neuroscience at Woods Hole MA. It has also been used in 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 2.4, became available in November 2014, and continues to be updated. The most recent packaged distribution is the May 2019 update and PGENESIS 2.4 official release. It 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 under development.

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