GENESIS (software)
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Original author(s) | Dr. James M. Bower |
---|---|
Initial release | 1988 |
Stable release | |
Repository | |
Written in | C[2] |
Operating system | Unix-like, macOS, Windows (using Cygwin)[2] |
Type | Simulation environment |
License | GPL[3] |
Website | genesis-sim |
GENESIS (The General Neural Simulation System) is a simulation environment for constructing realistic models of neurobiological systems at many levels of scale including: sub-cellular processes, individual neurons, networks of neurons, and neuronal systems. These simulations are “computer-based implementations of models whose primary objective is to capture what is known of the anatomical structure and physiological characteristics of the neural system of interest”.[4] GENESIS is intended to quantify the physical framework of the nervous system in a way that allows for easy understanding of the physical structure of the nerves in question. “At present only GENESIS allows parallelized modeling of single neurons and networks on multiple-instruction-multiple-data parallel computers.”[5] Development of GENESIS software spread from its home at Caltech to labs at the University of Texas at San Antonio, the University of Antwerp, the National Centre for Biological Sciences in Bangalore, the University of Colorado, the Pittsburgh Supercomputing Center, the San Diego Supercomputer Center, and Emory University.
Neurons and Neural Systems
GENESIS works by creating simulation environments for constructing models of
History
GENESIS was developed by Dr.
How GENESIS Works
GENESIS is useful in creating a simulation environment for constructing models of neurobiological systems, such as:
- sub-cellular processes
- individual neurons
- networks of neurons
- neuronal systems
The GENESIS system is complicated, but relatively easy to use.
An individual can input commands through one of three ways: script files, graphical user interface, or the GENESIS command shell. These commands are then processed by the script language interpreter. "The Script Language Interpreter processes commands entered through the keyboard, script files, or the graphical user interface, and passes them to the GENESIS simulation engine. The simulation engine also loads compiled object libraries, reads and writes data files, and interacts with the graphical user interface".[8] Below is a graphical representation of the user input process and a sample GENESIS output.
Applications
Most current applications for GENESIS involve realistic simulations of biological systems. It is usually used to simulate the behavior of larger brain structures, for example the
GENESIS can be used in combination with
GENESIS has been used in many studies.
There may also be biomedical applications of the software. For example, St. Jude Medical in Europe has developed an implanted GENESIS device.[11]
See also
- Neural network software
- Artificial intelligence
- Artificial neural network
- Integrated development environment
- Theoretical neuromorphology
- NEURON
Publications
- The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation System, Springer, (1998), ISBN 978-0-387-94938-3
References
- ^ a b "The GENESIS 2 simulator home page". GENESIS project. Retrieved 26 December 2015.
- ^ a b "Platforms". GENESIS project. Retrieved 1 October 2016.
- ^ "The Ultimate GENESIS 2.3 CDROM Distribution". GENESIS project. Retrieved 26 December 2015.
- ^ (Bower, Beeman, and Hucka. GENESIS Simulation Software. 1998)
- ^ (A consumer guide to neuronal modeling software TRENDS IN NEUROSCIENCES 15: 462-464, 1992 Copyright © Elsevier Science Publishers Ltd, (UK), 1992 E. De Schutter Division of Biology 216-76, California Institute of Technology, Pasadena, CA 91125, USA)
- ^ a b c d e f (Introduction to Neurons and Neuronal Networks John H. Byrne, Ph.D., Department of Neurobiology and Anatomy, The UT Medical School at Houston)
- ^ staff (2019-04-17). "Vintage Video: The Paragon Supercomputer - A Product of Partnership". High-Performance Computing News Analysis | insideHPC. Retrieved 2023-10-27.
- ^ (Bower, Beeman, and Hucka. GENESIS Simulation Software. 1998.)
- ^ (Bhalla, U.S. (2002).Use of Kinetikit and GENESIS for modeling signaling pathways. In: Methods in Enzymology, ed. Hildebrandt, J.D and Iyengar, R. Academic Press, 345, 3-23.)
- ^ "GENESIS Publications". Archived from the original on 2012-12-25. Retrieved 2012-11-19.
- ^ Video: GENESIS Implanted Device