the Biocomputing Survival Guide is available in its version 2.0 as
'beta test'. This document is intended to serve as a cookbook for
the casual user of computers in molecular biology.It is not inten-
ded to explain science or make the programs' algorithms more
The Guide starts with general introductory remarks on computer
usage and trouble shooting. Softwarewise, the material focuses
mostly on the Wisconsin Sequence Analysis Package from Genetics
Computer Group, Inc., 575 Science Drive, Madison, Wisconsin, USA
53711. Excerpts from the Program Manual for the Wisconsin Package,
Version 8, copyright 1994 by Genetics Computer Group, by permis-
sion of Genetics Computer Group.
The previous versions of the Guide were available only as PC-based
word processor format. Learning from the past, the new version is
written in a new format which requires a separate application to
generate RTF, LaTEX, or HTML files, as we need wordprocessor, high
quality typesetting, and the famous WWW type of documentation as
Why another format ?
The JAM (Just Another Metafile) format allows to adapt the Survival
Guide to any individual site in a few minutes. All you need is to
modify a few files and process these in the 'jam' processor, which
is an application known to run on many opreating systems. The modi-
fications are so easy that they can be made even by the end user.
If you decide that you don't need site-specific modifications then
you do not need to modify anything,just select options (see below).
The JAM, STE, INT and TEC files are available as binary, UNIX-com-
pressed set or individually by anonymous FTP,and there are binaries
and source code files for the JAM processor. JAM uses the NCBI VIB-
RANT Toolkit (Kahns et al., NCBI) which is required to compile and
link the GUI version of the JAM processor. JAM compiles either with
or without GUI on all platforms we use here in the laboratory (DEC
VMS & OSF/1,IRIX,Mac,Dos, Windows). We provide binaries of the jam
processor (with the GUI included) for AXP/VMS, OSF/1, IRIX, Mac,
Dos and Windows. We are confident that jam compiles on any vanilla
system as long as it is providing a compiler for the C language. On
FTP, we provide some examples in RTF and DVI format, and a WWW
site to view the HTML on- line.
Options to be selected in JAM without modifications required
The VMS or UNIX operating system, or 'international' or 'site-spe-
cific' layout, as well as the format, are all selectable with the
GUI (click and play) or the commandline version (try and enjoy).
Additionally, features like SRS, ATLAS, ENTREZ etc can be toggled
easily without knowing how to use an editor.
So this is the listing of the files you might want to modify:
Data for local site contatcs
ACCESS.STE: This file holds the procedures used to access the
site, i.e. how to use a terminal server via LAT, or what
name to give as TCP/IP host.
ACCOUNT.STE: Information whom to contact and who is eligible for
being serviced at the local site.
GCG.STE: How to start the GCG program packge.
BLAST.STE: How the BLAST suite of programs is run, and where the
actual processing takes place, and what databases are
available within BLAST.
ENTREZ.STE: How the ENTREZ suite of programs can be accessed.
PROFILES.STE: How 'profile' methods are used
SWSEARCH.STE: How programs using the 'Smith and Waterman' algo-
rithm are accessed.
BLOCKS.STE: Information on the availability of protein motif da-
tabases other than PROSITE, such as BLOCKS or PRODOM.
DATABASE.STE: Description of the (GCG) type databases available
at this site.
The Guide is available on-line as Hypertext on the Swiss EMBnet
node WWW server as
<a href= http://www.ch.embnet.org/jam/jam.html > Jam Page </a>.
The ftp archive is bioftp.unibas.ch, directory survival/ . Please
note that you should only use the survival/ directory. Thank you.
N O T E
We call this a 'beta' version. If you find any problems, please
let us know. The current HTML version can also write 'reflector'
and 'receptor' files. These are not ready yet for general re-
Acknowledgements: The program writing was supported by Basel
University, and the Swiss National Science Foundation (NF).
R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078|
Biocomputing CH 4056 Basel| electronic Mail doelz at ubaclu.unibas.ch|
Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
<a href=http://beta.embnet.unibas.ch/>EMBnet Switzerland:info at ch.embnet.org</a>