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
