EMBOSS: Project Meeting (Fri 28th November 2003)


HGMP: Alan Bleasby, Gary Williams, Hugh Morgan
Lion: Thomas Laurent
Cambridge Uni:
EBI: Peter Rice, Martin Senger, Marie-Laetitia Denayer

Apologies: Rodrigo Lopez Tom Oinn Jon Ison Lisa Mullan

Minutes of the last meeting

Minutes of the meeting of 14th November 2003 are here

1. Action points

1.1 From this meeting:

2.8.0 release (AJB, 2003-11-28)
EMBOSS Ontology commit (PMR, 2003-11-28)
newcoils/pepcoil merged program (PMR, 2003-11-28)

1.2 From previous meetings:

Convert graphics to grout (PMR, 2003-09-19)

1.3 No longer required:

Investigate WIKI FAQ list (DC, 2003-09-19)
Done: See item 2.3

Read and comment on EMBOSS Quick Guide for Gary (action all, 2003-10-17)
Done: Comments passed to Gary and Tim.

2. Software Development

2.1 EMBOSS 2.8.0 release

Alan has fixed problems with file input end-of-line characters, and with string handling, in MacOSX.

Gary has updated the documentation for all programs, including ACD changes and report output.

Alan and Peter have worked through the contributions to the emboss-submit mailing list, and have committed those that are suitable for the 2.8.0 release. The "newcoils" program is added as a "make check" program for now. We should merge this with "pepcoil".

2.2 EMBOSS Ontology

Marie described her EMBOSS ontology. This was a 6-week student project to define an ontology for ACD input and output types and ACD definitions. The ontology is produced in Protege, and will be committed in the documentation directory as 3 XML files and a description.

Marie has suggestions for extending ACD. Then Ontology will need to be maintained to track furtuire ACD changes. One key issue is what name to give the ontology when it is committed.

2.3 Wiki

Damian has announced the EMBOSS Wiki starting page. There is no content so far.

2.4 Hardware acceleration

Alan has a contact interested in developing hardware acceleration for EMBOSS. First steps should be to profile the library code and algorithms to find suitable candidates for hardware acceleration, and for software acceleration (e.g. using macros instead of expensive or frequently used functions).

3. Documentation & Training

3.1 Documentation specialist

Alan reported that Damian has submitted a job description and draft advertisement. This is now waiting for MRC head office administration.

3.2 Books

Final decisions on the contracts should be made soon.

3.3 Other books

Peter has been asked to update the EMBOSS DNA analysis chapter for the Christoph Sensen "Biotechnology 5b: Genomics and Bioinformatics" book for a new edition.

Peterhas promised to look into providing an article on EMBOSS for a Public Library of Science journal http://www.publiclibraryofscience.org/

The EMBOSS Quick Guide for EMBnet is almost ready to submit.

4. Administration

4.1 ISMB Tutorials

Alan and Jon are planning a programming tutorial.

Peter is planning an installation/administration tutorial, to include web (probably wEmboss), GUI (Jemboss) and werb service (SoapLab) interfaces.

Lisa was volunteered to provide a users' view of EMBOSS.

Clare Sansom is planning a young scientists' SIG for CCP11 also at ISMB.

4.2 SourceForge

Peter and Tom have reviewed thebug-tracking facilities on SourceForge. Peter will set up bug and feature request lists after the 2.8.0 release. Everyone on emboss-bug will need a sourceforge login to work on these lists. Peter and Tom are already registered.

4.3 Queries

Peter will work on the union/splitter submissions from Kim Rutherford at Sanger.

Gary will look into the large input for eprimer3 problem after 2.8.0.

Peter considers Ville's problems with bad EMBL/SwissProt format should be investigated after 2.8.0, and probably left as it is.

Peter will look into providing codon usage and otehr local data files in Nexus format after 2.8.0.

Peter will look into cirdna/lindna input as a new report format after 2.8.0.

Peter asked the emboss list about clashes between database names and input filenames. The conclusion was to leave the present situation, where the database name is used.

Peter will investigate the bugs in est2genome, prettyplot and diffseq after 2.8.0 as no other users have reported these problems. Alan will create and emboss-announce mailing list for use after 2.8.0.

5. AOB

Alan will pick a date, probably early January, for the annual EMBOSS dinner.

6. Date Of Next Meeting

Next meeting to be held at 9.30 on December 12 2003, Pompeiian Room, Hinxton Hall