EMBOSS: Project Meeting (Fri 14th November 2003)


HGMP: Alan Bleasby, Jon Ison, Gary Williams, Damian Counsell, Lisa Mullan, Claude Beazley
Lion: Thomas Laurent
Cambridge Uni:
EBI: Peter Rice, Tom Oinn

Apologies: Rodrigo Lopez

Minutes of the last meeting

Minutes of the meeting of 31st October 2003 are here

1. Action points

1.1 From this meetings:

1.2 From previous meetings:
MEME documentation is required (action AJB, 2003-02-21)
Provide documentation for prophecy (AJB, 2003-03-21)
Investigate WIKI FAQ list (DC, 2003-09-19)

Read and comment on EMBOSS Quick Guide for Gary (action all, 2003-10-17)

1.3 No longer required:
Done: Comments passed on to Gary.

2. Software Development

2.1 EMBOSS 2.8.0 release

Alan has completed the configuartion changes for 64 bits, and completed the new indexing code (to go live in 2.9.0). EMBOSS is working on Fedora, and MacOSx X11 graphics are working again.

Peter found and fixed the bug in "supermatcher". It was a multi-statement line which changed meaning ni the code cleanup. A thorough check showed no other such problems in the code.

Peter reported QA tests are running cleanly, and most memory leaks (all minor) have been fixed.

Alan and Peter will work through the outstanding emboss-submit contributions.

Jon has a new application "rocplot" (not yet committed) to produce statistics for the quality of prediction methods. Inputs are a list of ranked hits or mulitple lists of hits. Peter suggested making these two programs to make the definition of inputs and outpus for workflows and GUIs simpler.

The release should be by the end of the month.

2.2 EMBOSS Ontologies

Tom requested extensions to ACD to describe task ontologies describing the output of a program run in terms of the operations performed on the input data. EMBOSS has some of this information, but not in sufficient detail. This will be used by taverna to provide workflow provenance.

2.3 Other

Alan reported IBM want the old machine back, but before it goes they are interested in benchmarks of the old and new machines. The timing of the QA test run would be a useful example.

3. Documentation & Training

Damian and Terry presented a DocBook introductory course this week.

Documentation is to be transformed into DocBook by the 3.0.0 release.

4. Administration

4.1 Queries

The list of emboss-bug and other queries was reviewed.

5. AOB

6. Date Of Next Meeting

Next meeting to be held at 9.30 on November 28th 2003, Pompeiian Room, Hinxton Hall