EMBOSS: Project Meeting (Aug 16th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Val Curwen, Thon de Boer, Mark Faller, Jon Ison, Sinead O'Leary

1. Matters Arising


2. General progress on release 0.0.4

HGMP have added "iep", "pepstats", "digest", "backtranseq", "cusp", "trimseq", "msbar", "showdb" and are working on "getorf".

Alan has added the "ajcod" module to AJAX for codon usage calculations. and random number routines in "ajmath".

Alan has added "embiep" and "embprop" modules to NUCLEUS.

Alan has added an "OR" function to ACD processing. Peter will add an "AND" function to complement this.

Sequence features ("-ufo" etc.) have been added to ACD processing. Peter will pass details to Thon de Boer for the ACD documentation.

Michael Schmitz has reported problems on a Linux installation with ACD processing. Peter is investigating.

Peter has fixed a duplicate definition in ajmath.

Peter is investigating memory leaks in sequence reading.

Sequence begin and end processing has some problems. Peter will check that these are reset by ajSeqreplace and look into other cases.

Postscript graphics output is crashing when the graph title is defined.

The SGI machine used for the nightly builds has been upgraded to Irix 6.5

Peter was at ISBM '99 in Heidelberg. The DKFZ (the German EMBnet node) have implemented an early release of MEBOSS into their W2H HTML interface. Peter will work with Peter Ernst at DKFZ on improving this.

There was a BioPerl meeting at ISMB where there was support for a Perl front end to EMBOSS. Richard will make a first attempt at this.

Also at ISMB were Netgenics, who are implementing Perl interfaces to their Synergy package and could automatically convert ACD into their Perl code. Peter will work with them on this.

Peter has promised the IMGT database group that EMBOSS will support IMGT as a sequence database. The format is similar to EMBL.

3. Preparation for Beta Release

HGMP have been recommending EMBOSS to their users for specific problems and have had favourable reports.

A new version of "readseq" is due soon that will handle feature tables. Peter will look into porting some of the code into EMBOSS, although it is written in Java now.

Peter will revise the database setup documentation and pass on to Thon de Boer.

Peter will continue to work through the documentation for other applications.

4. Any Other Business

5. Next meeting

Next meeting Monday 23rd August, 11:00am, usual place.

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