This is a summary of recent developments which have been announced to the BABEL mailing list. This file will be updated from time to time in order to announce new features available on BABEL and the latest additions to the BABEL directories.
The latest version of the Purkinje cell tutorial (Release 2-2.16), which implements the full De Schutter and Bower (1994) detailed Purkinje cell model, may be found in the BABEL "tutorials" directory. This may be used to replace Release 2-2.11 in the GENESIS 2.3 distribution. In the new version, multiple cell views are now possible via the output menu, and a configuration layer on top of the tutorial allows you to restrict the GUI to the things that you think are important.
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.
Please note that there are two Sourceforge home pages for GENESIS development and access to the public forums. You may want to set browser bookmarks for them.
http://sourceforge.net/projects/genesis-sim is the main site for GENESIS 2 development. Although it's unlikely that there will be a GENESIS 2.4 release, the CVS repository will be kept up-to-date with the most recent bug fixes. GENESIS 2 Help forum postings are automatically sent to babelnews and, at the discretion of the babelnews moderator, some of them are sent to the mailing list. The recent posts on compiling GENESIS 2 under Mac OS/X are examples.
http://sourceforge.net/projects/moose-g3 is the site for MOOSE and GENESIS 3 development. You may download the latest development releases of MOOSE and GENESIS 3 from that site. Requests for new GENESIS features should be directed to the forums under that project.
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 lastGENESIS 2 release, as we hope to begin preliminary releases of GENESIS 3 sometime in 2006.
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 beta release for GENESIS 2.3 is now available for testing at the Sourceforge site for GENESIS development http://sourceforge.net/projects/genesis-sim.
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, and revised 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 next year.
The BABEL objects directory now contains a GENESIS implementation of the Izhikevich modified integrate and fire neuron. With this model, four parameters A, B, C, and D can be used to produce a wide variety of action potential shapes and firing patterns, with greater computational speed than the usual compartmental cell models. This contains documentation, instructions for compiling it into GENESIS, and demos of cell and network simulations using the 'izcell' object.
The genesis-cygwin directory contains a version of GENESIS 2.2.1 that has been modified to run under Microsoft Windows, using Cygwin. Cygwin is a free Windows application that provides a UNIX-like environment for Windows. This package contains a precompiled executable "genesis.exe" and GENESIS libraries, the usual documentation and simulation scripts, and the modified GENESIS source code, patched with the August 2004 bug fixes. Additional documentation contains instructions for getting, installing, and using Cygwin, installing GENESIS from the provided genesis2.2.1-cygwin-bin.tar.gz file, and optionally patching or recompiling GENESIS. A short guide to "Getting Around in UNIX for Windows Users" has also been provided to help those who are not familiar with the UNIX command line environment.
The Bug-fixes directory has been updated to 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. This includes the previously announced "varargs" patch, which will be needed for installing GENESIS under Fedora 2 Linux.
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 BABEL home page.
The hypertext archive of babelnews postings on BABEL is now being updated automatically.
The hypertext archive of babelnews postings on BABEL has been updated through May 2004. The BABEL Bug-fixes directory has patches to fix some problems compiling GENESIS 2.2.1 under recent compiler and operating system versions. Experimental patches are also available in the BABEL directories for compiling under Mac OS/X and on machines using 64 bit AMD processors.
The hypertext archive of babelnews postings on BABEL has been updated through December 2003.
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 BABEL web site.
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 BABEL 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.
GENESIS version 2.2.1 is now available, and we recommend that all GENESIS users upgrade to the new version. This release has a new version of the kinetics library and the Kinetikit scripts (kkit version 9). It fixes a number of bugs in version 2.2, and also has a large number of changes to fix compilation problems with newer OS versions, compiler versions, and libraries. Two new debugging commands, gctrace and gftrace, have been added. Although the documentation has not been changed since version 2.2, you can find a description of these commands and other changes from version 2.2 in the file genesis/src/CHANGES.
The BABEL archives directory also contains Parallel GENESIS (PGENESIS) version 2.2.1. This release, which replaces PGENESIS 2.2, incorporates some bug fixes to the July 2001 2.2 version, and to the January 15, 2002 2.2a version. 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 hypertext archive of BABEL mailing list (babelnews) postings has been updated through April 18, 2003.
Alfonso Delgado-Reyes' latest patches and binaries for running GENESIS 2.2 under Mac OS X can be found in the BABEL GENESIS22-MacOSX directory.
The Introductory through Advanced Tutorials on Neural Modeling presented at GUM*02, Nov. 8, 2002, San Antonio, TX are available in the BABEL gum-tutorials directory.
A beta release of GENESIS version 2.2.1 is now available on BABEL in the "archives" directory, which you can access from the BABEL web page through the "Browse the BABEL directories" link. It is contained in the file genesis-2.2.1-beta-20020812.tar.gz. This release is primarily a bug-fix upgrade from version 2.2, with the addition of two new debugging commands gctrace and gftrace.
With the relocation of the Bower laboratory from Caltech to the University of Texas at San Antonio, BABEL and GENESIS are 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. Although mail to the old Caltech addresses will be forwarded for a period of time, 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.
Postings to babelnews should go to babelnews@genesis-sim.org.
The new BABEL web page and archives can be accessed at http://www.genesis-sim.org/BABEL/. This is a passworded web page with the usual BABEL username/password. Instead of having a passworded BABEL ftp site, as in the past, we are now making access to the BABEL directories through the web page using http, instead of ftp.
Let us know (by email to babel@genesis-sim.org) if the lack of command line ftp access to BABEL presents a problem for any of you.
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 either the GENESIS home page or the BABEL directories page from the BABEL web site. 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 in the BABEL archives directory.
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 Babel Newsletter #9. 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.
[Other ancient news has been removed.]