EMBOSS: Project Meeting (Mon 6th September 10)
1. Minutes of the last meeting
Minutes of the meeting of 23rd August 2010 are
2. Maintenance etc.
Jon has completed the EDAM annotation of the EMBASSY packages.
Documentation has also been improved for the one line descriptions and
short descriptions for EMBASSY packages.
Alan is investigating whether there is a satisfactory way to
configure gsoap. The library requires that the user defines
a handful of functions in their own code. This presents
problems in linking legitimate applications that do not
require those functions. One can end up with either
missing functions or circular dependencies. The gsoap library
sadly does not allow registration of callback functions.
Jon reported that documentation has now been produced for the
true minimum/failrange/maximum ACD mechanism, allowing developers
the choice of how applications behave when given inappropriate
Michael is making the Ensembl functions available to the
EFUNC/EDATA system. He is making extensive function naming changes in
order to fit the EMBOSS naming schema/rules.
The Trend Micro anti-virus software has reported a false-positive
hit for mEMBOSS-184.108.40.206-setup.exe. Investigations by David Bauer
have shown that the false signature comes from the embossdata.exe
file. He has informed Trend Micro and Alan has made the file
available to them.
3. New developments
3.1 Access methods
Mahmut has been investigating DAS, pending the resolution of the
GSOAP issues mentioned above. He has working development code
to integrate single fully specified DAS sources via DB
definitions. He is investigating making the definitions
more generic as is done for (e.g.) ensembl database
specifications, allowing one definition to be the root of
several sources. Parsing of the returned XML from
ajseqread will either require ajdas.c/h files in the core
library or callbacks using code in the ajseqdb library. It is currently
coded using the former less-convoluted, and therefore preferable, approach.
It was also noted that HTTP access is becoming more commonplace in the
AJAX libraries. Alan can investigate moving the HTTP primitives, from
the ajaxdb library, into the core library. That would provide an
opportunity to integrate the new URL code and integration of
username/password code into the HTTP access methods.
Jon has implemented some minor fixes to EDAM. He has also
provided notes for the EDAM/EMBRACE continuity web site. He
highlighted the forthcoming conference on Semantic Web Applications
and Tools for Life Sciences in Berlin. An abstract for EDAM/BioXSD has
been submitted for a workshop he and Matus are holding there.
Alan reported the power failure in the main machine room which
killed the EMBOSS file server. All data had to be recovered from backup
onto local disc and the backup software redirected accordingly.
All server services are now being provided by local workstations pending
the arrival of a replacement server.
5. Documentation and Training
C.U.P. have provided typeset example chapters for the books. It was
noticed that section numbering was too deep in some places in
the Developer's Guide. Also, tables were not referenced from
the fixed text. Jon has provided C.U.P. with corrected
6. User queries and answers
Alan will look at the possibility of users' ".embossrc" files being
read when using an authenticating Jemboss server.
8. Date Of Next Meeting
Next week is the GMOD meeting in Cambridge.
The next EMBOSS meeting will be on Monday 20th September.