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HASSLE TOOLS released

The Distributed Execution System hassle at comp.bioz.unibas.ch
Thu Sep 2 19:46:10 EST 1993


                                                     Basel, September 1, 1993

The  Swiss  Node  of  the  European  Molecular  Biology  Network  (EMBnet) is 
pleased  to  announce  the  availability  of  HASSLETOOLS.  The  Hierarchical
Access System for Sequence Libraries in Europe  (HASSLE)  has  been  released
recently.  The  TOOLS for this distributed network computing software include 
the following functionality in the first release: 

                 UNIX Customer   VMS Customer   UNIX Provider   VMS Provider
Search sequence
with BLAST            x              x              x

Search sequence
with FASTA                           x              x                x

Retrieve sequence
with FETCH            x              x              x                x


Both Provider and Customer software are available in full source and are ex-
tensively documented  (HASSLE; about 130 pages, HASSLETOOLS; about 45 pages).
The software  was  developed on the IRIX operating system (Silicon Graphics) 
for  the  various  UNIX  flavours  and  on the AXP operating system (Digital 
Equipment) for the VMS sites.

The following operating systems have been verified to run HASSLE: 

VMS System         Customer   Provider     UNIX System    Customer  Provider
VMS 5.4  UCX 1.3      X                    IRIX 4.0x        X         X 
VMS 5.4  UCX 2.0      X                    IRIX 5.0x        X         X
VMS 5.5  UCX 2.0      X           X        Sun OS 4.x       X         X
VMS 5.4  Multinet 3.0 X           X        Ultrix 4.x RISC  X         X
VMS 5.5  TCPWare 3.1  X                    Ultrix 4.x VAX   X
VMS 5.5  Multinet 3.2 X           X        OSF/1            X         X
AXP 1.0  Multinet 3.2 X           X        Convex 10.1      X
AXP 1.5  UCX 3.0      X           X
AXP 1.5  Multinet 3.2 X           X
AXP 1.5  TCPWare 3.2  X           X
 
The currently  available  tools  focus  on  the  integration into the software 
environment  of  the  Genetics  Computer  Group  (GCG) Inc, Madison, Wisconsin. 
To run the BLAST Provider, the NCBI BLAST suite must be  installed  also.  The
BLAST frontend does NOT access the NCBI Blast  Server.  GCG  must be installed
in order to use HASSLETOOLS.

The software is available free of charge from bioftp.unibas.ch or, preferably,
from  the  mirror   nic.switch.ch (in  the mirror/embnet-ch directory). You are 
encouraged to develop  own  TOOLS to raise the functionality.  We will demo the 
software on this year's business  and  workshop  meeting of EMBnet, and provide 
help in installation at that time if required. 

Regards
Reinhard Doelz
EMBnet Switzerland







                       D I S C L A I M E R 
========================================================================

     ***********************************************************
     *                                                         *
     *                      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.,Basel University 1992. The HASSLE  protocol) *
     * if results to be published are obtained.  All  software *
     * accessed with the system is copyrighted  separately  by *
     * the corresponding vendors and  needs  to  be  cited  in *
     * publications. See the file NOTE.ME for more information.*
     ***********************************************************


Literature references: (Status August, 1993) 

     Doelz, R.: Hierarchical Access System for Sequence Libraries in 
	Europe (HASSLE). A tool to access sequence databases remotely. 
	Computer Applications in the Biosciences, accepted. 

     Doelz, R.:  HASSLE. A Software to manage Distributed Processing 
        on Heterogenous Systems. Computer Networks for Research in Europe, 
	a quarterly supplement to Computer Networks and ISDN Systems, Suppl. 
	2, (1993), Elsevier Science Publishers B.V., accepted.


========================================================================


Code structure: 

HASSLE should be clearly separated in several modules. Each module 
is described briefly at the beginning of each file. 


         +-------------------+  +-----------------------------+
         |  hassle programs  |  |   (other client/server sw)  |
         +-------------------+  +-----------------------------+
         +--------------------------+ +-----------------------+
         |   CLIENT functionality   | |  SERVER functionality |
         +--------------------------+ +-----------------------+
         +------------------------------------+ +-------------+
         | Network layer (processing I/O etc) | |  Utilities  |
         +------------------------------------+ +-------------+
         +----------------------------------------------------+
         |   Transport layer (TCP/IP and other protocols)     |
         +----------------------------------------------------+



EXAMPLES: 
=========
[Note that part of the output is generated by original GCG code which 
is used within HASSLETOOLS to achieve the best integration possible. 
The HASSLETOOLS distribution does not include this code; this implies
that the GCG source must be available on the computer where HASSLETOOLS
are expected to be installed.]


$ blast

BLAST does a very fast similarity  search for word-identity between a
query sequence and a given sequence database.  BLAST answers the
question, "What sequences in the database are very similar to my sequence?"
The BLAST program suite is much faster than FASTA and WORDSEARCH,
but BLAST programs are, sometimes,  less sensitive.

 support file: "Blastdata.Dat".

 BLAST with what query sequence ?  protein:mchu

                  Begin (* 1 *) ?
                End (*   149 *) ?

***  Sequence  protein:mchu is a protein  (* YES *) ?

 Do you want to search with the program

    A) BLASTP (peptide vs. Protein Data Base)
    B) TBLASTN (peptide vs. translated DNA Data Base)

 Please choose one (* A *):

 Do you want to search
     A) nr:* protein database (remote/yeti.embnet.unibas.ch)
     B) swissprot:* protein database (remote/yeti.embnet.unibas.ch)
     C) tfd:* protein database (remote/biomed.uio.no)

 Please choose one (* A *):

 What should I call the output file (* Mchu.Blast *) ?

 *** Using BLAST default Parameters ***
 ***  for all non-specified fields  ***

BLAST frontend R.Doelz Version VMS 4.0.0

 ** blast will run as a batch job.

 ** blast was submitted to the batch queue using the VMS command:
    "  submit/noprint/notify/queue=yogi_bio/log=sys$scratch  "

Job BLAST_015512 (queue YOGI_BIO, entry 860) started on YOGI_BIO



$ fasta

FASTA does a Pearson and Lipman search for similarity between a
query sequence and any group of sequences.  FASTA answers the
question, "What sequences in the database are similar to my sequence?"
The relationship between FASTA and WORDSEARCH has not been
characterized, but FASTA is faster and, sometimes, more sensitive.

 FASTA with what query sequence ?  protein:mchu

                  Begin (* 1 *) ?
                End (*   149 *) ?

 Search for query in what sequence(s) (* SwissProt:* *) ?

 What word size (* 2 *) ?

 List how many best scores and alignments (* 40 *) ?

 What should I call the output file (* Mchu.Fasta *) ?

 ** Fasta will run as a batch job.

 ** Fasta was submitted to the batch queue using the VMS command:
    "  @hasslestuff:decide.com  "

requested job is: fasta
initialisation file: fasta_015630.init
Local:protein Remote:protein
Local:swissprot Remote:swiss
Output: mchu.fasta
Job scheduled for remote execution.
Job FASTA_015630 (queue YOGI_BIO, entry 861) started on YOGI_BIO

$ 

% fetch 

FETCH copies GCG sequences or data files from the GCG database 
into your directory or displays them on your terminal screen.

 FETCH what sequence(s) ?  swiss:calm_human

... Trying Network ...Support data file is: "support.dat".
 Checking resources ... 
found database SWISS at HASSLE4.EMBNET.UNIBAS.CH ...............

HFETCH HASSLE frontend R.Doelz Version $Id: hfetch.f,v 4.4 93/08/30 18:22:06 doelz B4-0-0 $
----- This is HASSLE version D4-0-0 (93/08/12) 
----- (C) Biocomputing Basel, 1992, 1993
NOTE: HASSLE used on host bioy.embnet.unibas.ch
ERROR: Server cannot process correctly HFETCH request
REDIRECT received due to BUSY (overloaded).
NOTE: HASSLE used on host BIOX.EMBNET.UNIBAS.CH
ERROR: Server cannot process correctly HFETCH request
REDIRECT received due to BUSY (overloaded).
NOTE: HASSLE used on


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