HASSLE 4.1 released

EMBnet Switzerland embnet at comp.bioz.unibas.ch
Mon May 23 17:50:47 EST 1994


                                                          Basel, May 22, 1994

The  Swiss  Node  of  the  European  Molecular  Biology  Network  (EMBnet) is 
pleased  to  announce the  availability of the Hierarchical Access System for 
Sequence Libraries in Europe,  HASSLE,  release 4.1.  

HASSLE currently runs on many EMBnet hosts and covers features like FASTA and
BLAST searching, PROFILESEARCH and MOWSE searching, and other tools of biolo-
gical interest.  This  post is meant to address system administrators who are 
interested  to  run  own  services, or end users who would like to make their 
administrators interested.  

Both Provider and Customer software are available in full source and are  ex-
tensively  documented  (postscript; about 120 pages, dvi or full LATEX source 
alternatively). The software was originally developed  on  the IRIX operating 
system (Silicon  Graphics)  but to maintain optimal conditions at our site we 
switched to the OSF/1 operating system (Digital Equipment). Starting from the 
base  code,  we made it run by adding modifications for the various UNIX fla-
vours and on the VMS  operating system (Digital Equipment) for the VMS sites.
A AXP/VMS system running UCX TCP/IP services was used for the original setup,
but other emulations are supported as well. 

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        HP/UX            X
AXP 1.5  Multinet 3.2 X           X        LINUX            X
AXP 1.5  TCPWare 3.2  X           X        Solaris 2.3      X         X
                                           IBM AIX          X         X
 
Most of the currently available tools  focus  on  the  integration into the 
software environment  of  the  Genetics   Computer  Group  Package (Version 
7 currently,Version 8 coming later this year) (GCG Inc, Madison, Wisconsin) 
Other  tools  feature general sequence retrieval or make use of other soft-
ware, such  as the MOWSE server in the UK (UK EMBnet node) or the dedicated
hardware BIOCELLERATOR (compugen Ltd, Rehovot) (Israelian EMBnet node).  

The  software  is  available  free of charge from bioftp.unibas.ch or, pre-
ferably, 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 meeting of EMBnet,associated
to the 3rd international GPC conference in Chester. HASSLE was described in
the January issue of CABIOS.  



"NOTE.ME" file follows 

i
         ***********************************************************
         *                                                         *
         *                      H A S S L E                        *
         Hierarchical Access System for Sequence Libraries in Europe
         *                                                         *
         ***********************************************************


                   V E R S I O N   4 . x   ,    1 9 9 4

===========================================================================
The HASSLE  protocol  and its associated software modules Customer, Master,
Responder,  and the local  processing programs ( used collectively with the
name HASSLE in the following text) in its current Version 4 are copyrighted
by Biocomputing Basel, and available freely without cost.

The distribution of the software shall strictly follow the following rules:
o HASSLE  may  not be sold, as a  whole  or  in  pieces. HASSLE code may be
    used, adopted,  incorporated in any program package, commercial, share-
    ware or public domain, as long  as the provider of this program package
    makes sure that (a) the HASSLE layer is always up to date with the cur-
    rent HASSLE release version and (b) the incorporation is performed in a
    fashion that  allows to access the source code, or use HASSLE as provi-
    ded by the original distributor Biocomputing Basel.
o HASSLE may not be used in a  commercial  environment in order to generate
    profit from services which are accessing the services available via the
    HASSLE protocol.
o HASSLE may be adopted by  any  service  provider, commercial, non-profit,
    academic, or  any  other, in the understanding that the provider offers
    services  to the community without charge within the limits of reasona-
    bility. Exceeded limits may not be used as argument to charge  for  the
    service (see above).
o HASSLE source code is available for the  current  version  4. In order to
    keep the communication layer free of trouble,  any  deviation  from the
    protocol specifications (on port 375) is prohibited. Source code fixes,
    changes, enhancements etc. are most welcome if  documented and communi-
    cated to the  authors. After evaluation, the  changes  will possibly be
    considered in a new full release version or immediately released as in-
    cremental version if a bug fix is required.
o HASSLE may be placed on any file server, as long as it is made sure that
    the distribution and documentation are kept up-to-date.
o HASSLE  customers  and  providers  should always send the registration as
    distributed with  the  package  in order to be informed and kept up-to-
    date with the development and announcements.
===========================================================================

         ***********************************************************
         *                                                         *
         *                      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.                                           *
         ***********************************************************

  +---------------------------+-------------------------------------------+
  |    Dr. Reinhard Doelz     | Tel. x41 61 2672247    Fax x41 61 2672078 |
  |      Biocomputing         | electronic Mail       doelz at urz.unibas.ch |
  |Biozentrum der Universitaet+-------------------------------------------+
  |   Klingelbergstrasse 70   | EMBnet         embnet at comp.bioz.unibas.ch |
  |CH 4056 Basel  SWITZERLAND | Switzerland       gopher.embnet.unibas.ch |
  +---------------------------+------------- http://beta.embnet.unibas.ch/


Thanks:
To  Ute,  Juergen  and Marianne for the patience; for the funding contribu-
tions  from   Basel  University,  Schweizer Nationalfonds, Silicon Graphics
and  Digital  Equipment;  and  various suggestions, contributions, and code
fragments from (alphabetically) K.Adelmann, R.Appel, F.Eggenberger,M.Egger,
J.Epstein,T.Etzold,the whole GCG Team,D.Gilbert,A.Godknecht,M.Hage,R.Harper,
P.Linder,R.Lopez,H.Moeller,R.Omond,F.Roesel,L.Rosenthaler,P.Stoehr,P.Zimak.

$Id: NOTE.ME,v 1.3 94/02/27 19:04:20 doelz B4-1-0 $
    
Special thanks for version 4.1 go to 
Jeroen Coppieters, University of Gent (HASSLE AIX)
Martin Kroeker, TH Darmstadt (HASSLE AIX, ascomp bug)
Giompieno Marcenano, University of Genua (HASSLE HP/UX)


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

This is HASSLE 4.1 full release (D4-1-0) and for internal
and external use. The fortran-written tools are NOT updated.

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-


CHANGES TO HASSLE 4.0:

fixed/changed:
--------------
table size problem indicating faulty table member in nslookup
changed names in uppercase to avoid double table population
customer does no longer die upon rejected transmission
customer does no longer die if local file not found in responder mode
customer does no longer die upon wait time expiration
customer does report on routine in upper layers rather than exit silently


removed:
--------
DUMB compilation directive (was unsupported anyway)
WAITFOR statement for other than CUSTOMER


added:
------
-o (/only_dumb) flag
-n (/nodumb) for MASters to reject , can be enforced as default by
        specifying -DNODUMB
-l (/local) for local configuration file
-z 504 for report on commandline flags
add WAITFOR implementation in client.c
add SWITCH recognition in client.c
add WAITFOR recognition in asyn.c
add DUMB to SERVICE file (in hassle.com/hassle.csh recognition)
allowed client module to read absolute pathnames
added local configuration file capability
added INSTANT HASSLE as binary distribution; this one can't do servers

AIX and LINUX, as well as SOLARIS, now run fine

to be done:
-----------
API documentation in detail
documentation update
tools update (must wait for GCG 8)
HP/UX
cleanup of code and detailed exit status
update service (transmission of binaries)
and a lot of others


ADDED AFTER BETA 4.1
-=-=-=-=-=-=-=-=-=-=-=

removed bug in ascomp (thanks Martin Kroeker)
added HP/UX

  



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.


-- 
 
+----------------------------------+-------------------------------------+
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