Genesis

GENESIS stands for GEneral NEural Simulation System. This simulation program originated at CalTech about 12 years ago, and has been steadily evolving. GENESIS is a ubiquitous simulator, enabling the user to model at many different levels, from subcellular components to single neurons to small networks. GENESIS models can be programmed in script, and by a flexible, interactive XODUS GUI in an object-oriented manner. (XODUS stands for X-based Output and Display Utility for Simulators.) GENESIS is widely used in the computational neurobiology community, and there is a clearly written text available describing how to use it, with examples (Bower and Beeman, 1998). Most GENESIS applications appear to be at the microlevel; i.e., detailed neural models of single neurons of small assemblies of neurons such as found in models for central pattern generators (CPGs). Such detailed models include soma, dendrites, axon, synapses, and many different ion channels. GENESIS allows user selection of five integration routines: forward Euler, backward Euler, exponential Euler (the GENESIS default), Adams-Bashford, and Crank-Nicholson.

When GENESIS is used to simulate very large arrays of neurons, the parallel processing form of GENESIS, PGENESIS can be used. GENESIS is used to define neuron properties in the large network, then PGENESIS is used to run the simulation efficiently. Information about PGENESIS can be found at the Pittsburgh Superconducting Center web site: www.psc.edu/general/software/packages/pgenesis/project_ docs/pgenesis-home.html.

GENESIS runs exclusively on UNIX OS machines and their variants. Recently, it was adapted to run under LINUX on 486 and Pentium PCs. The interested reader wishing to investigate GENESIS further should visit the URLs: http://www.bbb. caltech.edu/GENESIS, http://www.bbb.caltech.edU/hbp/database.htmlandhttp://www. caltech.edu/hbp/GOOD.

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