A new version of the GENESIS Neural Modeling Tutorials package is now available for viewing or downloading from the GENESIS web site, http://www.genesis-sim.org/GENESIS/. These are an evolving package of HTML tutorials intended to teach the process of constructing biologically realistic neural models with the GENESIS simulator.
Precompiled binary GENESIS distributions for OS/X on Intel-based Macintoshes are now available for download from http://sourceforge.net/projects/genesis-sim. This is in addition to the existing binaries for OS/X on PowerPC architectures (MacOSXDarwin), Windows/Cygwin, and Linux.
GENESIS version 2.3 is now available for download from the GENESIS web site (http://www.genesis-sim.org/GENESIS). GENESIS 2.3 supercedes version 2.2.1, and has a number of changes in the simulator source code to allow use on a greater variety of platforms including Intel and AMD 64 bit processors, MacIntosh with OS/X, and Microsoft Windows with the Cygwin environment. It includes Kinetikit Version 11, Version 2 of the Purkinje cell tutorial, some new objects and enhancements of existing ones, plus revised and updated documentation. We expect that GENESIS 2.3 will be the last GENESIS 2 release, as we hope to begin preliminary releases of GENESIS 3 sometime in 2006.
Binary distributions are also available that include precompiled versions of the 'genesis' and 'nxgenesis' (GENESIS without X11 graphics) executables. At present these are for Linux, Microsoft Windows with Cygwin, and Mac OS/X.
The new release of Parallel GENESIS (PGENESIS 2.3), which now has support for MPI as well as PVM, is also available. PGENESIS should run on almost any parallel cluster, SMP, supercomputer, or network of workstations where MPI and/or PVM is supported, and on which serial GENESIS itself is runnable.
The Bug-fixes directory has patches to fix some problems compiling GENESIS 2.2.1 under recent compiler and operating system versions. This will be of particular interest to those installing GENESIS under Fedora or SuSE linux. Other fixes address some problems with the kinetics library, for compilation under non-Linux systems such as IRIX and Solaris, and some subtle errors with the adaptive stochastic calculations.
The Book of GENESIS, originally published as a Springer-Verlag imprint, is now out of print. As the publisher does not plan to reprint the book, the copyright has been reclaimed by the authors, and we are now able to offer it to be downloaded from the GENESIS web site.
The NIH has just approved 5 years of funding for GENESIS support, maintenance and further development. You can read about our future plans for GENESIS by following the link on the GENESIS home page.
A precompiled version of the GENESIS 2.2.1 distribution is now available for Linux on Pentium-class ("x86") PCs. The easiest way to get GENESIS up and running on this platform is to download the file genesis2.2.1-linux-bin.tar.gz from the "binaries" directory on the GENESIS web or ftp site and follow the directions in the accompanying README file. This will allow you to a perform a complete installation of GENESIS without having to edit the Makefile and compile it. The genesis executable has been statically linked, so it should be useable on any recent version of x86 Linux.
There is also a new release of Parallel GENESIS (PGENESIS 2.2.1), designed for networks of workstations (NOW), symmetric multiprocessors (SMP) and massively parallel processors (MPP). This release, which replaces PGENESIS 2.2, incorporates some bug fixes to previous versions. It can be run on any platform which supports GENESIS 2.2.1 and the PVM (Parallel Virtual Machine) software. When used with GENESIS version 2.2 or later, it allows GENESIS to be run on networks of workstations (NOW), symmetric multiprocessors (SMP) and massively parallel processors (MPP). PGENESIS is described further in Readme.pgenesis.
The Introductory through Advanced Tutorials on Neural Modeling presented at GUM*02, Nov. 8, 2002, San Antonio, TX are available on the GENESIS website.
With the relocation of the Bower laboratory from Caltech to the University of Texas at San Antonio, GENESIS is moving too. To reflect the fact that GENESIS development now takes place at many locations around the world, we have chosen an address that is not specific to any one institution, genesis-sim.org. Mail to the old Caltech addresses will be forwarded only for a limited period of time, so please make note of and use these new addresses:
The main GENESIS web site is http://www.genesis-sim.org/GENESIS/ The GENESIS ftp site may be accessed either through this web page, or by anonymous ftp to genesis-sim.org (/pub/genesis).
Email about GENESIS, bug reports, etc. should be addressed to genesis@genesis-sim.org.
Inquiries concerning GENESIS Users Group (BABEL) memberships, address changes, etc. should be sent to babel@genesis-sim.org.
Finally, we would like to announce the availability of some bug fixes for GENESIS 2.2 and PGENESIS 2.2. A description of the bugs and the replacement files can be found by following the Bug Fixes link on the GENESIS home page. The PGENESIS 2.2 distribution has been replaced by a new 2.2a distribution (pgenesis.2.2a.tar.gz and .Z) that includes the PGENESIS fixes. It is available on the GENESIS ftp site.
GENESIS version 2.2 is now available. This release includes many new features and enhancements to previous versions. For a short summary of new features, see the README file in this directory. Further details are given in genesis/src/CHANGES, and genesis/Doc/Changes.doc.
This directory also contains Parallel GENESIS (PGENESIS) version 2.2. This release, which replaces PGENESIS 2.1, has been updated to be compatible with GENESIS 2.2. It can be run on any platform which supports GENESIS 2.2 and the PVM (Parallel Virtual Machine) software. When used with GENESIS version 2.2 or later, it allows GENESIS to be run on networks of workstations (NOW), symmetric multiprocessors (SMP) and massively parallel processors (MPP). PGENESIS is described further in Readme.pgenesis.
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