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Biocomputing Survival Guide,V2.0b

Reinhard Doelz doelz at comp.bioz.unibas.ch
Sat Oct 8 12:37:51 EST 1994


Colleagues, 

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 
transparent.

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
well. 

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. 
Setup
   GCG.STE: How to start the GCG program packge. 
Searching procedures 
   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. 
Databases
   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-
lease. 



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> 



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