Organization of the BABEL directories

Each of these directories has a README file describing the contents. New files are continually being added, so it is advisable to log in periodically and look around. Notable developments will be summarized in the latestnews.html file. More details can be found in the hypertext archive of postings to the babelnews mailing list.

Book of GENESIS - Downloadable Internet Edition

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 internet at no cost.

cells

Various cell models that have been implemented with GENESIS

contrib

This directory is intended as a temporary storage place for user-contributed files. Files placed here will be periodically reviewed and placed in appropriate permanent locations. We encourage you to submit documentation notes, GENESIS scripts, source code for new GENESIS objects or functions, or anything else which you would like to contribute to BABEL. This is most conveniently done by emailing an attached gzipped or compressed tar file, along with an explanation, to babel@genesis-sim.org.

education

Information and materials relating to the use of GENESIS in education. We urge you to send course syllabi, exercises, or any educational materials that make use of GENESIS to babel@genesis-sim.org for inclusion in this directory.

examples

Contains a number of short example scripts which illustrate various features and "tricks" with GENESIS.

models

GENESIS scripts for user-contributed models (other than single cell models, which are in the cells directory).

newdocs

This contains recently written pieces of GENESIS documentation which are not included in genesis/Doc. These will eventually be incorporated into the next release of the "official" GENESIS documentation. In addition it contains files with informal notes regarding the use of various GENESIS features.

objects

The subdirectories here contain source code and instructions for compiling and linking new GENESIS objects. User-contributed objects that are not included in the GENESIS distribution may be found here. (NOTE: Some of these have now been incorporated into GENESIS 2.3.)

tutorials

This directory and its associated subdirectories contain both text files and GENESIS scripts for exercises and tutorials that have been created since the publication of "The Book of GENESIS", and are not part of the GENESIS Neural Modeling Turorials package. It also contains updated versions of tutorials that are normally found in the GENESIS 2.3 Scripts/tutorials directory, such as the Purkinje cell tutorial.

utils

Contains stand-alone utility programs which may be used with GENESIS.

Older material related to earlier versions of GENESIS

NOTE: With the release of GENESIS and PGENESIS 2.3, many of the directories below are now obsolete. GENESIS 2.3 compiles under UNIX/Linux, OSX and Cygwin and now runs on Intel and AMD 64 bit processors. Binaries are available on the Sourceforge GENESIS 2 development web site for Linux, OS/X, and Windows/Cygwin. PGENESIS 2.3 incorporates the contributed patches for use with MPI.

Bug-fixes

This directory contains corrected files, patches and descriptions of the fixes for bugs or compilation problems with GENESIS. Be sure to look here before reporting any problems compiling or installing GENESIS.

binaries

The file genesis2.2.1-linux-bin.tar.gz is a version of the GENESIS 2.2.1 distribution that contains precompiled Linux executables for "genesis", the "convert" utility (in bin/convert), and the GENESIS object libraries in the lib directory. This is in addition to the usual directories for Scripts, Doc, src, etc. This will allow you to easily install GENESIS on Linux systems without having to edit the Makefile and compile. The README file in this directory should tell you everything you need to know to install it. If you are using IRIX, Solaris, or the old SunOS 4, you could also use the binaries compiled for the old GENESIS 2.1 release in the binaries/genesis-2.1 directory. (If someone wants to make and contribute statically linked 2.2.1 versions for these platforms, we will be happy to include them here.)

genesis-cygwin

This 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.