October 15, 1999
==================
The Bug-fixes directory now contains a file irix-6.5.patch that
solves some problems compiling GENESIS under IRIX 6.5, and also includes
fixes for other problems described in Irix64.compile. These patches
should be applicable to all IRIX versions.
It has been reported that the setup for hsolve elements fails under
SuSE Linux 6.0, and that this problem is corrected by applying the patch
for Red Hat Linux 6.0. (see below)
August 6, 1999
===============
An important patch needed to compile GENESIS under Red Hat Linux 6.0 is now
available in the Bug-fixes directory. See compiling.problems and
redhat-6.0.patch.
March 5, 1999
=============
If you experience problems in compiling or installing GENESIS (particularly
with recent versions of Red Hat Linux), be sure to look at the latest
additions to the Bug-fixes directory. The file "compiling.problems"
contains information and fixes for many common problems.
January 23, 1998
================
There are some problems compiling GENESIS 2.1 on SGIs with 64-bit binaries,
and problems with the display of graph axes. The file Irix64.compile in the
Bug-fixes directory describes the solution, and the file
GENESIS2.1-Irix64-fixes.tar.gz (or .Z) provides some patched replacement
files.
August 22, 1997
===============
GENESIS version 2.1 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 a much improved release of Parallel GENESIS (PGENESIS 2.1), designed
for networks of workstations (NOW), symmetric multiprocessors (SMP) and
massively parallel processors (MPP). This release, which replaces the
experimental version which was previously available on this site, can be run
on any platform which supports GENESIS 2.1 and the PVM (Parallel Virtual
Machine) software. PGENESIS is described further in Readme.pgenesis.
November 6, 1996
================
The GENESIS distribution has been updated to version 2.0.2, which includes a
number of bug fixes, ability to run on DEC Alphas, some new features
(described in genesis/src/CHANGES), and improved documentation which is now
available in hypertext (HTML) form.
May 10, 1996
============
We have recently discontinued the requirement of a registration fee for
membership in the GENESIS users group, BABEL. Now, all that we require is
some assurance that you have a serious interest in using the GENESIS
simulator. The README file in this directory contains information on
joining BABEL.
November 17, 1995
=================
The GENESIS distribution has been updated to version 2.0.1, which includes a
number of bug fixes, new features (described in genesis/src/CHANGES), and
support for the 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)
An updated version of the parallel GENESIS libraries, with support for the
Cray T3D, 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.
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.
September 6, 1995
=================
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
distribution. The following two files have the same contents as
genesis.tar.Z, but are more efficiently compressed.
size name description
==== ==== ===========
1237725 gendisk1.tgz - the genesis directory tree, without Doc and Scripts
879296 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.
August 11, 1995
===============
This directory now contains the
August 1995 distribution of GENESIS, version 2.0.
Information about this new release is contained in the README file in this
directory. Version 2.0 represents a major revision of GENESIS from the
previous version (1.4.2). If you have used a previous version of GENESIS,
please read the file genesis/Doc/Changes.doc.
This directory also contains the first release of Parallel GENESIS,
designed for networks of workstations (NOW), symmetric multiprocessors
(SMP) and massively parallel processors (MPP). This release is known
to run on SGI/Irix and has run on these workstations: Sun4/Solaris,
Alpha/OSF1.3, DecStation/Ultrix4.3, Sun4/SunOS. It has run on these
SMPs: SGI-Challenge/Irix 5.3, Sun4MP/Solaris. It will soon be ported
to the Cray T3D/E MPP and later to Intel Paragon and IBM SP2 MPPs.
If you wish to compile the parallel libraries for GENESIS, you will need to
download the following files, in addition to the GENESIS 2.0 distribution:
pargenesis.R1.tar.Z - parlib source
pvm3.3.6.tar.Z - pvm3.3.6 source
pvm_userguide.ps.Z - pvm user's guide
For more information about GENESIS and "The Book of GENESIS", you may access
the GENESIS World Wide Web Server, http://www.bbb.caltech.edu/GENESIS. This
will allow you to see "snapshots" of GENESIS simulations, take a look at the
manual, and find information about research which has been conducted with
GENESIS.
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