FarFetch sites?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Sun Jul 24 08:14:51 EST 1994


Mike Mitchell (mike at bison.lif.icnet.uk) wrote:
: As far as I am aware there is only one server for FarFetch
: (farfetch.unh.edu). Are there other servers? Please email
: responses to me, if there is sufficient interest I will post
: a compilation of sites (if any!)


Some Nodes of the European Molecular Biology network (EMBnet) have achieved 
to run a different service which is more flexible than 'farfetch' due to 

	* several servers
	* general concept (runs other services like FASTA, BLAST, etc). 
	* fault tolerance 
	* load balancing 

All you need to do is get the corresponding client installed and you can 
run several 'tools' easily. 

The service is called the 'Hierarchical Access System for Sequnece Libraries 
in Europe', abbreviated HASSLE. Servers are in Norway, UK, France, Switzer-
land, Israel  and Greece. Services are 
 
FASTA 	- fasta services 
BLAST 	- blast suite, run on a 'nr' database based on EMBL 
MOWSE   - Molecular Weight Database searching 
SWSEARCH- Biocellerator in Israel 
PROFILE - Biocellerator in Israel 
FETCH   - entry retrieval 
MEDFETCH- Medline entries (given a Swissprot ID) 

 
HASSLE has been published in the January issue of CABIOS 1994, and is 
a registered world-wide IP protocol since mid-1992. It is copyrighted, 
free software and can be obtained from the ftp server nic.switch.ch 
in the mirror/embnet-ch/bioftp-sw/hassle directory. Full source, as well 
as extensive documentation, is available. Binaries have been compiled 
for a limited number of platforms to speed the installation if desired.
Some services are shell/command file scripts, some require a fortran com-
piler and a valid GCG license (Version 7, currently). 

EXAMPLE installation of a 'fetch' tool: 
=======================================

% ftp nic.switch.ch
Connected to nic.switch.ch.
...
Name (nic.switch.ch:doelz): ftp
331 Guest login ok, give your e-mail address (user at domain) as password.
Password:
...
ftp> cd mirror/embnet-ch/bioftp-sw
ftp> ls
200 PORT command successful.
150 Opening ASCII mode data connection for .
-rw-rw-r--  1 28        16             202 May  1 15:53 README
drwxrwxr-x  2 488       16             512 Jul  7 09:10 dbcomp
drwxrwxr-x  6 28        16             512 May 28 21:12 hassle
drwxrwxr-x  4 28        16             512 Feb 27 22:15 hassle_old
drwxrwxr-x  2 28        16            1024 May  1 21:06 hassletools
drwxrwxr-x  3 28        16             512 Feb 27 22:16 hassletools_old
226 Transfer complete.
ftp> cd hassle/binaries
ftp> ls
200 PORT command successful.
150 Opening ASCII mode data connection for .
-rw-rw-r--  1 28        16              96 May  1 15:57 0README
-rw-rw-r--  1 28        16          164352 Mar 20 18:54 HASSLE.AXP_MULTINET
-rw-rw-r--  1 28        16          168448 Mar 20 18:45 HASSLE.AXP_TCPWARE
-rw-rw-r--  1 28        16          158720 Mar 20 17:15 HASSLE.AXP_UCX
-rw-rw-r--  1 28        16          112128 Mar 20 18:50 HASSLE.VAX_MULTINET
-rw-rw-r--  1 28        16          114688 Mar 20 18:20 HASSLE.VAX_UCX
-rw-rw-r--  1 28        16            6064 Mar 20 18:55 NOTE.ME
-rw-rw-r--  1 28        16           60416 Mar 20 17:15 SUPER.AXP
-rw-rw-r--  1 28        16           38400 Mar 20 18:20 SUPER.VAX
-rw-rw-r--  1 28        16          428969 Mar 27 10:40 hassle.CONVEX
-rw-rw-r--  1 28        16          316920 Mar 20 14:30 hassle.IRIX4
-rw-rw-r--  1 28        16          290581 Mar 20 16:40 hassle.OSF1
-rw-rw-r--  1 28        16          169476 Mar 20 14:24 hassle.SOLARIS
-rw-rw-r--  1 28        16          237568 Mar 20 16:48 hassle.SUNOS
-rw-rw-r--  1 28        16          357932 Mar 20 17:04 hassle.ULTRIX
-rw-rw-r--  1 28        16          114560 Mar 20 14:30 super.IRIX4
-rw-rw-r--  1 28        16          111314 Mar 20 16:40 super.OSF1
-rw-rw-r--  1 28        16           58936 Mar 20 14:27 super.SOLARIS
-rw-rw-r--  1 28        16           65536 Mar 20 16:47 super.SUNOS
-rw-rw-r--  1 28        16          112580 Mar 20 17:04 super.ULTRIX
226 Transfer complete.
ftp> bin
200 Type set to I.
ftp> get hassle.OSF1 hassle
150 Opening BINARY mode data connection ... 
...
ftp> cd ../../hassletools
ftp> get README.hfetch README.hfetch
...
ftp> get hfetch.csh hfetch.csh
...
ftp> quit
%

Next, edit the file hfetch.csh and change the line 

setenv HASSLELOCATION   .... 

to your directory. 
If you are done with this, make all files executable and do a 

% hfetch.csh
FETCH gets an entry from a GCG database. Please 
give the name as database:entry code, e.g. OWL:calm_human
swissprot:cade_mouse
--- INSTANT HASSLE B4-1-0p (94/03/05) (C) Biocomputing Basel 1992-1994
NOTE: BIOX.EMBNET.UNIBAS.CH is used as provider.
WARNING:  Provider cannot process HFETCH request ... REDIRECT received due to NOSERVICE.
NOTE: BIOZ.EMBNET.UNIBAS.CH is used as provider.
ERROR: Provider cannot process correctly HFETCH request
REDIRECT received due to NOWAY.
NOTE: YETI.EMBNET.UNIBAS.CH is used as provider.
NOTE: Listening for reply from YETI.EMBNET.UNIBAS.CH on port 15036 for result
TE: Answer from host yeti.embnet.unibas.ch [131.152.8.3], port 1780 ...Result for service HFETCH 

NOTE: Received file fetch.log 

NOTE: Received file cade_mouse.sw 
NOTE: JOB       15036    completed 


as you can see, three different nodes have been contacted before a successful 
retrieval occured. The installation is similarly easy for other operating 
systems, including VMS. Please note that a more luxory verion is available 
if you bother to use the fortran tools. The 'fetch' integrates into the 
normal GCG environment (GCG 7, and fortran compilers are required).




Example of the (installed) modified fetch on VMS(GCG/fortran version):
=======================================================================

$ fetch genembl:zmrncal

FETCH copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
... Trying Network ...Support data file is: "Support.Dat".
 Checking resources ...
...found database GENEMBL at BABY.URZ.UNIBAS.CH .............
HFETCH HASSLE frontend R.Doelz Version 30/08/93 B4-0-0
--- HASSLE version A4-2-2 (94/06/22) (C) Biocomputing Basel 1992-1994
NOTE: BABY.URZ.UNIBAS.CH is used as provider.
ERROR: Provider cannot process correctly HFETCH request
REDIRECT received due to BUSY.
NOTE: YETI.EMBNET.UNIBAS.CH is used as provider.
NOTE: Listening for reply from YETI.EMBNET.UNIBAS.CH on port 15037 for result
NOTE: Answer from host yeti.embnet.unibas.ch [131.152.8.3], port 1793 ...Resultfor service HFETCH

NOTE: Received file fetch.log

NOTE: Received file zmrncal.em_pl
NOTE: JOB       15037    completed


The GENEMBL is biredundantly updated on daily (EMBL) and weekly (genbank)
basis. Accession numbers can be used as well. 




Regards
Reinhard 

DISCLAIMER
Note that  the software  mentioned  resembles  Computer  Program(s)  which 
require a license in order to be run unless stated otherwise in  a  state-
ment  codistributed with the software. The use of the program(s) was  men-
tioned  within  a specific problem or example and must not be used to con-
clude that other  software products cannot possibly do a similar job. 

 
         ***********************************************************
         *                                                         *
         *                      H A S S L E                        * 
         Hierarchical Access System for Sequence Libraries in Europe
         *                                                         *
         *                                                         *
         * This program package has been written starting from '92 *
         * at the Biocomputing Laboratory, University of Basel, by *
         * Reinhard Doelz. Valuable  suggestions from various col- *
         * leagues, including code contributions (as  documented), *
         * allowed to make this code portable, and  running on the *
         * different platforms.  Though it has been a major effort *
         * to make the HASSLE protocol suite and its  tools  work, *
         * no   responsibility  can   be  taken for  errors  which *
         * might occur while running or result from processing the *
         * program's output. The program writing was supported  by *
         * Basel University, and a grant from the  Swiss  National *
         * Science Foundation (NF). The software resembling HASSLE *
         * may be copied and resdistributed only if this statement *
         * is  preserved.  HASSLE  may not, as a whole or in part, *
         * sold or used by commercial institutions to gain  profit *
         * from the services accessed on the basis of academic re- *
         * search. Users should acknowledge  the  program  package *
         * (Doelz, R., Hierarchical  Access  System  for  Sequence *
         * Libraries in Europe (HASSLE): a tool to access sequence *
         * databases  remotely.  Comput-Appl-Biosci. 10(1), 31-35, *
         * 1994)  if  results  to  be published are obtained.  All *
         * software accessed with the system is copyrighted  sepa- * 
         * rately by corresponding vendors and need to be cited in *
         * publications.                                           *
         ***********************************************************

HASSLE is currently being  rewritten  at  the  Biocomputing Laboratory by 
Reinhard Doelz,  Florian Eggenberger and  Chris Wadley. More services are 
expected to be available in the near future. 



-- 
  +---------------------------+-------------------------------------------+
  |    Dr. Reinhard Doelz     | Tel. x41 61 2672247    Fax x41 61 2672078 |
  |      Biocomputing         | electronic Mail       doelz at urz.unibas.ch |
  |Biozentrum der Universitaet+-------------------------------------------+




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