|
SRS 5.0.5
Introduction
SRS (Sequence Retrieval System) is an indexing system which gives access to virtually all databanks available in a text (ASCII) format. An important feature is its ability to combine all indexed databanks into a network where new ways of linking information from different sources can be explored. In the former releases a start was made to integrate databanks with sequence analysis tools such as BLAST or FASTA for sequence similarity searches and CLUSTALW for multiple sequence alignment.
Version 5.0.5 is the first version where all buttons and hypertext links in SRSWWW should be functional. This includes the SAVE button!
We added a command line option for wgetz that will allow us to download all information about all databanks of your server. Please create .it files for databanks you add (see 'SRSDB:template.it' and 'SRSDB:swissprot.it' for an example).
We added menus, check lists, multiple selects to the query forms - we are sure it is an improvement in some cases but maybe not always - please give us feedback!
As an incentive for you to write .i, .is and .it files you can see them now in color through the 'databank information page'.
Differences in detail:
Added menus, check lists and multiple select lists to query forms in SRSWWW. This can be customised in the ".i" files using attribute .guiInfo of $field and $srsfield and $guiInfo.
Added a new function 'PageFlatInfo' to wgetz so that all information about all databank sserved by SRSWWW can be obtained via a WWW call. This is the foundation for building the 'database of databanks' which will appear once a 'critical mass' of SRS5 servers has been installed.
The 'Save' works finally from a single entry, entry list and query manager.
All buttons and hypertext links in SRSWWW should now be fully functional.
Many little problems have been fixed in the ".i" and ".is" files and a few have been added (not problems but .i and .is files!).
The .i, .it, .is pages accessible through the 'databank information page' can now be seen in color which is done by 'SRSICA:colicarus.i'
The files 'SRSDB:srsdb.i' and 'SRSDB:srsgen.i' can be also accessed in the 'databank information page'.
All Icarus examples in the SRS documentation are also colorised.
Quite a few sections have been added to the chapter 'SRS Server Maintenance', however, they still need a bit of reviewing.
Subentries (features) from EMBLNEW, SWISSPROTNEW can now be safelydisplayed.
The sequence of protein databanks have now the correct size
The link to the status page has been replaced by a list of SRS5 servers which will be eventually have a link to the database of databanks.
All Icarus functions are now documented and listed within groups.
Known problems with this release:
High optimisation on OSF1 2.x, 3.x might give problems.
On Solaris cc or gcc can now be used. When using gcc a warning message
gcc: unrecognized option `-Xa' is now given and should be ignored.
There is a minor parsing error when installing the documentation - for us it is an old friend, but I guess it might be worrying if you haven't been introduced to it.....
man_capi.i:928: error: syntax error, production `l_proto' :
|INT4 (*ParGetFunction (char *parName))()|
.....^
no match with |^[a-zA-Z0-9_*]+|
Availability:
SRS 5.0.5 has been compiled and tested on IRIX 5.x, 6.x (32-bit binary), OSF1 4.x, Solaris. It should also work on SunOS, Ultrix and could work on AIX, HP-UX. The complete package can be downloaded from the EBI FTP-server.
Information provided by: Thure Etzold
Resources and further information
European Bioinformatics Institute
http://www.ebi.ac.uk/
SRSWWW server -- query databases now!
http://srs.ebi.ac.uk/
The SRS newsgroup
news:bionet.software.srs
Download SRS
ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.0.5.tar.gz
External sites are not endorsed by EMBL-EBI |
