EMBOSS: Project Meeting (May 24th 1999)

Attendees

Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Val Curwen, Thon de Boer, Mark Faller, Sinead O'Leary
EBI: Rodrigo Lopez
Apologies: Martin Senger

1. Matters Arising

2. General progress on release 0.0.4

Ian has added "pepwindow" for hydrophobicity plots and is now working on graphics.

Alan split "seac" into two applications, "fuzzpro" and "fuzznuc", for general pattern matching in protein and nucleotide sequences.

EnCompass (Tim Littlejohn) are interested in using EMBOSS with their BioNavigator interface.

SRS 6 is under beta test at the Sanger Centre. The latest beta version has application support so we can start to look at how EMBOSS can be best integrated.

EBI now has a CORBA server that can be used as an EMBOSS database.

Mark's clustalw implementation is added.

New examples of SRS servers and other database definitions are needed for the .embossrc documentation.

Some of the present ACD file documentation is long. The application documentation line should be brief, and also the help text as "wossname" and the "-help" output can be long in some cases.

3. Library documentation

Peter's draft documentation librray docuemntation is still in progress.

4. EMBnet Cuba Course

Dave Judge should be able to test EMBOSS this week for the Cuba course. Linux graphics may still need to be addressed.

5. Sequence Features

Richard is starting to work on sequence features in an "ajfeat" module with an abstract internal representation for DNA and protein sequence features.

EBI have started work to produce genome reference sequences. Peter Sterk and Guenter Stoesser are the contacts. The first reference sequence should be available in June.

6. Other applications

Bill Pearson is changing his old code and will have a rewrite late this year so may be best to wait before integrating the rest.

Alan is working on restriction digests.

7. Next meeting

Monday 31st is a holiday. Next meeting Monday 7th June, usual time and place.

Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.