EMBOSS: Project Meeting (Fri 30th April 2004)
Minutes of the last meeting
Minutes of the meeting of 19th March 2004 are
1. Action points
Action points dropped from the agenda.
2. Software Development
Alan has modified plplot to automatically test for plplot
variables. Should be no need to define PLPLOT_LIB in future releases.
2.2 Performance comparisons
Alan has tested wordmatch on Itanium II machnies with the HP
and Intel compilers. Run times on the test system for Yeast chromosome
III were 4.15 to 5.4 hours.
2.3 Code cleanup
Peter is working through library functions defining categories
(new, modify, etc.) for the main object type.
Attribute lists will need an "@cc" attribute to add comments between
sets of related attributes. This was done using comments in the code,
but to help convert codedatatypes into attributes the embossdoc parser
objects to comments in the typedef struct code.
Jon is updating directory functions in domainer and other
Alan is trying various compiler warning options. Xlc (AIX) is
very fussy. The SGI compiler is generating the most warning messages.
3. Documentation & Training
Peter has proposed an EMBOSS demo.
Lisa has proposed a
Jemboss demo. The date/time will change as
it was accidentally scheduled at the end of the conference.
3.2 April Developers Training Course
Feedback from the developers course was very good. One company are using
EMBOSS internally and report no need for GCG. Acadeic users are using
EMBOSS for education. BEN will contribute a blast wrapper, currently
site-specific but could be made more general.
A few docuemntation bugs were identified. The edata documentation
should return the elements of a data structure. A version of ajSeqNew
with an existing sequence was suggested as a copy constructor.
More coding examples are needed, and possibly more talks, in the next
Code examples can be put into the new "myemboss" EMBASSY package.
The July course is cancelled as everyone will be at ISMB in
Glasgow. Next developers course will be ni November.
Damian will send a couple of chapters for the user book to
check content etc.
EMBnet funds will not be available for the docuemntation project -
unclear what is happening to EMBnet funds. No further funds are
available for RFCGR/HGMP due to some limit in the current EMBnet contract.
Peter is contributing an updated EMBOSS chapter to a book
edited by Christoph Sensen for Wiley.
5. User queries and answers
Gary's current list reviewed. Most new issues were already answered.
7. Date Of Next Meeting
Next meeting at 9.30 on May 14, 2004,