EMBOSS: Project Meeting (Fri 30th April 2004)


RFCGR/HGMP: Alan Bleasby, Jon Ison, Gary Williams,
EBI: Peter Rice,


Minutes of the last meeting

Minutes of the meeting of 19th March 2004 are here

1. Action points

Action points dropped from the agenda.

2. Software Development

2.1 Plplot

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 domainatrix programs.

2.4 Compilers

Alan is trying various compiler warning options. Xlc (AIX) is very fussy. The SGI compiler is generating the most warning messages.

3. Documentation & Training

3.1 ISMB

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 course. 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.

3.3 Books

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.

4. Administration

No items.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. AOB

7. Date Of Next Meeting

Next meeting at 9.30 on May 14, 2004,