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       [_][_][_][_][_][_]                  THE GENESIS USER'S GROUP
       [_][_][_][_][_][_]          
       [_][_][_][_][_][_]                       NEWSLETTER #6
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     [][][][][][][][][][][]                   NOVEMBER 17, 1995
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This is to annouce some new additions to the babel directories, including GENESIS 2.0.1, Kinetikit, and updated Parallel GENESIS libraries.

GENESIS 2.0.1

We now have GENESIS version 2.0.1 available on babel. This is an upgrade to version 2.0, with the following changes, bug fixes, and new features:

GENESIS 2.0.1 now installs and runs on HP's (HPUX) and IBM RS6000s (AIX). As GENESIS has not had much testing on the RS6000, we would very much appreciate reports of your experiences installing and running GENESIS 2.0 on the RS6000.
several changes to support the initial release of the kinetics library and the kkit kinetics toolkit (described below).
Neurokit has some changes to allow the use of Ca_concen elments with hsolve (methods 10 and 11). Neurokit and Orient_tut have some changes to prevent long lines in the icon files from causing problems with SGI's. Squid resets to single pulse mode when doing voltage clamps.
Some addtional Doc/*.doc files have been added for synchan utility functions, and some others have been updated. Details are given at the end of the Doc/README file.
several fixes to the Makefiles to solve compilation and installation problems. Dependencies for install targets in all library makefiles have been removed. Additional instructions for workarounds of Solaris 2.4 and SunOS 4.1.[234] compile and link problems have been added to the main Makefile. A TMPDIR macro has been added to the main Makefile to allow specification of an alternate temporary directory for making GENESIS.
several fixes to the Usermake and Libmake makefile templates for compiling user libraries
The element path wildcard routines will now process white space separated lists of path specifications and include all elements matching each path. (Note that the commands still take a single wildcard path argument and that the path list must be passed in this single argument.)
Exp and log functions have been added to tables.
The setupalpha command now detects singularities and corrects those that can be corrected.
xcell now handles cells with symcompartments correctly.
Other changes are described in src/CHANGES.

The full 2.0.1 distribution is contained in the file genesis.tar.Z (a link to archives/genesis2.0.1.tar.Z). Alternatively, you may update version 2.0 to 2.0.1 with the patches contained in archives/genesis2.0.1-patch.Z. These should be installed with the "patch" utility from the genesis installation directory, NOT from the src directory. If you have trouble applying the patches, please download the new distribution.

Kinetikit

Kinetikit is a utility for modeling large numbers of chemical reactions such as occur in biochemical signaling pathways. It consists of two sections: the C-code library kinetics, which gets compiled and linked with GENESIS, and the script interface for kinetikit, also known as kkit. Kkit is designed to provide a user-friendly, click-and drag interface for kinetics modeling. In addition to defining and running kinetic models, it is intended to facilitate managing kinetic data in models of complex signaling pathways.

The files are contained in:

Kkit1.1.tar.Z - the C-code library and kkit.

kkit.bin.tar - GENESIS binaries compiled with the kinetics library for

various platforms (currently Solaris, Linux and SGI). (optional)

Updated Parallel GENESIS

We are pleased to announce that Parallel GENESIS has been ported to the Cray T3D and is available on the Pittsburgh Supercomputing Center T3D. This machine has 512 processing nodes, each a Dec Alpha with 64 Mb memory. For information on how to obtain accounts on this machine, see http://www.psc.edu/welcome.html or send email to grants@psc.edu Technical questions about use of Genesis on PSC's T3D should be addressed to Nigel Goddard (ngoddard@psc.edu).

Patch 1 contains the modifications necessary for the T3D together with some bug fixes for Solaris machines. We have successfully run Parallel GENESIS on a Solaris multiprocessor and the patch contains advice on steps necessary for this SMP. The patched version is contained in the file pargenesis.R1P1.tar.Z, which replaces pargenesis.R1.tar.Z. The patches themselves are available in pargenesis.R1.patch1.Z.

Alternate form of the GENESIS 2.0.1 distribution

For the convenience of of those with slow or unreliable ftp connections or who wish to transfer them to MSDOS format floppies (e.g. with mtools, SUN's PCFS, or with Linux), we have provided an alternate form of the GENESIS 2.0.1 distribution. The following two files have the same contents as genesis.tar.Z, but are more efficiently compressed.

     size   name           description
     ====   ====           ===========
   1249024  gendisk1.tgz - the genesis directory tree, without Doc and Scripts
    888893  gendisk2.tgz - genesis/Doc and genesis/Scripts

After being transfered to a UNIX system, they should be renamed to gendisk1.tar.gz and gendisk2.tar.gz and uncompressed with the gnu "gunzip" utility, then extracted with tar. This can be done with:

gunzip -c gendisk1.tar.gz | tar xvf -

On most Linux systems, it is possible to simply use:

zcat gendisk1.tgz | tar xvf -

Note that these *cannot* be uncompressed with the UNIX compress utility. If you do not have gunzip, use the genesis.tar.Z file, instead.

European ftp site for GENESIS

You may now get the GENESIS 2.0 distribution, as well as Kinetikit and the libraries for Parallel GENESIS by anonymous ftp from ftp://bbf-ftp.uia.ac.be/genesis. This is NOT a full mirror of babel, however.

Accessing babel:

You can access the babel directories by ftp to babel.bbb.caltech.edu (131.215.15.236), username "babel" and password "babelon". As before, we have no objections if this ftp account is used by other GENESIS users with whom you work. However, we ask you not to give out this access information indiscriminately.

The top directory ("/") is the main BABEL directory. You can use "ls" or "dir" to see what else is there, and "cd" to navigate through the directories. The README file describes the organization of the BABEL directories, and each subdirectory has ists own README file.

Dave Beeman - GENESIS Users Group
(dbeeman@dogstar.colorado.edu)
GENESIS WWW site - http://www.bbb.caltech.edu/GENESIS
Postings to babelnews: babelnews@bbb.caltech.edu
To communicate with babel: babel@bbb.caltech.edu