release of SRS5.0.3

etzold etzold at ebi.ac.uk
Thu Mar 13 17:40:50 EST 1997


Dear all,

after versions 5.0.1 and 5.0.2 which still had lots of problems we
consider
this to be the first stable version of SRS5. The distribution is now
available
on the ftp server at the EBI in Hinxton UK. If you have problems
accessing
it please let us know.

The file is at ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.0.3.tar.gz



Release notes:


SRS version 5.0.3
=================

SRS 5.0.3 has been compiled and tested on IRIX 5.x, 6.x (32-bit binary),
OSF1 4.x, Solaris.
It should work on SunOS, Ultrix and could work on AIX, HP-UX.


The numerous problems of version 5.0.2 concerning indexing and entry
access
should all be fixed.
The main differences to the previous release are the addition of an
'option bar'
in the entry display and the incorporation of analysis tools (BLAST,
FASTA,
Smith and Waterman search with the Bioccelerator and Clustalw). 
The way the applications are defined is still new and needs to be
documented.


Differences in detail:

1)  Many bugs concerning indexing and access to entries have been
removed.
    Indexing of GCG formatted databanks is now stable.
2)  The databank descriptions for many databanks, esp. the Transfacs and 
    Genbank has improved. 
3)  A few Icarus bugs have been fixed and also the error messages are 
    more informative. Both nodd and icarus should not dump core anymore.
4)  The example C programs in SRSDEMO have been revised and should all
work.
5)  The regular expressions have been reintroduced into the SRS query
language.
    (the documentation for the query language is still for version 4 but
has been
    extended for version 5 considerably).
6)  The chapter "SRS Server Maintenance" has been added to the online
    documentation system. It describes in detail how to set up a
separate WWW server
    that runs wgetz under its own account.
7)  in SRSWWW each single entry display contains an additional 'tool
bar'
    for linking the entry to other databanks, viewing the entry and
launching
    applications. 
8)  The applications BLAST, FASTA, SW (Smith & Waterman search with 
    Bioccelerator) and CLUSTALW have been added to SRS and can be called
from
    a the page containing a list of entries and a single entry.
Documentation of
    how to customize these applications and how to add more is still
lacking but 
    please have a look into SRSDB/genes.i. Every application is
described by an object
    $application. It has an Icarus command to build the command line and
one for launching
    the application. All the customization happens there.
    
10) The "SRS group" has moved to the EBI in Hinxton!;-)

Known problems with this release:

1) The "Save" option in SRSWWW does still not work properly.
2) Customization of the applications is easy but still not documented.
4) The $application objects in appl.i for the four applications BLAST,
FASTA, CLUSTALW
   and SW have been rewritten several times. It is possible that some
default
   values don't make much sense or are missing - please check and let us
know if you
   find bugs.
3) getz and wgetz can extract feature sequences but it is still not
possible
   to modify their begin and end positions as in SRS4.


--
Thure Etzold,   etzold at ebi.ac.uk
Giorgio Verde, verde at ebi.ac.uk
13. March, 1997




More information about the Bio-soft mailing list