Emergent Properties of Networks of Biological Signaling Pathways
Downloading GENESIS and Kinetikit
Source: Science. 1999 Jan;283(5400):381-7.
What is GENESIS?
GENESIS (General Neural Simulation System) is a general purpose simulation platform which was developed to support the simulation of neural systems ranging from complex models of single neurons to simulations of large networks made up of more abstract neuronal components. GENESIS has provided the basis for laboratory courses in neural simulation at both Caltech and the Marine Biological Laboratory in Woods Hole, Massachusetts, as well as several other institutions. 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.
Platforms supported
GENESIS and its graphical front-end XODUS are written in C and run under UNIX on Sun workstations (SunOS 4 or Solaris 2), DECstation (Ultrix), Silicon Graphics (Irix 4.0.1 and up) or x86 PC (Linux or FreeBSD) machines with X-windows (versions X11R4, X11R5, and X11R6). IBM RS6000s (AIX), HPs (HPUX), DEC Alphas (OSF v2 and v3, and Alpha Linux), and the Cray T3D have successfully been used for compiling and running GENESIS.
GENESIS Web sites
The main GENESIS Web site is at Caltech, with full source, extensive documentation, and many example scripts. GENESIS versions 2.1 and higher include Kinetikit.
Binaries and demonstration versions of the scripts used in the scripts are below.
These may be used to run the demonstrations for this paper, but are only a small subset of the full GENESIS distribution. However, they may be easier to install.