EMBOSS: Project Meeting (Fri 8th July 2005)


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


1. Minutes of the last meeting

Minutes of the meeting of 13th May 2005 are here

2. Software Development

2.1 Database indexing

Peter has some additional clues to formatdb output format for BLAST databases - but far from complete documentation.

2.2 PolyA sequences

Corell Duvall (attended the developers course) has contributed code for finding polyA sites in cDN, developed with Peter Ernst at DKFZ.

3. Administration

3.1 CVS commits

Alan proposed temporarily suspending access for those who commit changes that break builds for everyone else. The 5 fines are not enough deterrent. Unanimously accepted.

3.2 Mailing Lists

Peter reported discussions at BOSC where Hilmar Lapp asked for more projects to use Open Bio Foundation resources. Alan contacted Chris Dagdigian about moving the EMBOSS mailing lists to open-bio.org.

Alan reported that a new machine at Open Bio will be given the address emboss.open-bio.org.

FTP access on open-bio.org will be easy to maintain - much simpler than SourceForge's update system.

Mailing lists will transfer before the release on July 15th. Alan will ask whether RFCGR/HGMP can redirect mails sent to the old addresses, as Laurent Falquet (SIB) has not yet taken over the embnet.org addresses.

The mailing list move will be announced as soon as possible to give users a chance to change over. All existing subscribers will be moved.

3.3 Release 3.0.0

Alan requested a clear 2 days to prepare the release distributions and test them.

dbx indexing programs are now part of the main build, but announced as a beta release.

Peter will review all documentation on the sourceforge website and generate the TFM documentation for the distribution.

Alan has updated configure.in to release "3.0.0", and has added version numbers to the Ajax and Nucleus libraries to reduce problems with old versions.

Jon is reviewing all domainatrix tests.

Peter has updated the date for all test runs and example output to be 15th July 2005 at 12 noon.

Alan has updated the FAQ list to cover X11 and amd64 issues.

4. Documentation & Training

4.1 Books

Peter talked to the CUP stand at ISMB. They seemed happy and understanding over the delay in submitting the books.


Peter reported on the BOSC and ISMB conferences. Peter gave a talk on EMBOSS at BOSC, and a demo at ISMB well attended, with many US-based people new to EMBOSS. The demo included various interfaces and an example of developing a modified version of matcher using myemboss.

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 July 22nd, 2005,