EMBOSS: Project Meeting (Nov 29th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich, Ewan Birney
HGMP: Alan Bleasby, Gary Williams, Mark Faller, Val Curwen, Sinead O'Leary

1. Matters Arising


2. General progress on release 0.0.4

EMBOSS is now available from the Sanger CVS server.

Jose-Ramon Valverde (EMBnet Spain) has offered his calculus and algorithm library code to EMBOSS.

Peter is waiting for a reply on MSE licensing.

Peter will update the ajstr.c code to make all strings constant in functions where the pointer value will not change. This should be general policy as there have been two recent bugs caused by changed pointers which the compilers will only spot if they are declared "const AjPStr".

Peter still has to implement URLs as valid USAs.

Alan has "reANSIfied" AJAX library code.

Now that graphics code is split from the rest of AJAX, Ewan Birney is interested in using EMBOSS code in the new release.

The application documentation should include a table of valid qualifiers with descriptions, as for "antigenic". Peter will try to add most of the missing detail to ACD processing so that the table can be generated automatically.

Sinead has added "findkm" for enzyme kinetics.

Alan has added "oddcomp" from David Martin (EMBnet Norway).

Gary is working on "showseq", and also on a character based menu system called "esme"

Alan and Sinead have incorporated Keith Vass's suggestions into "prima". It still needs to be added to Makefile.am to become part of the main applications.

Peter has added "dbigcg" though it is not yet complete to index GCG formatted sequence databases using EMBLCD/Staden style index files.

Similar applications will be able to index blast1 and blast2 files (dbiblast1n, dbiblast2n, db1blast1p, dbiblast2p) and flat files (dbiflat). The code to parse entry names, accession numbers and offsets is unique to each, but the code to build these into the index files will be common. Mark wil be working on the database updating at HGMP.

"infoseq" and "geecee" can be retired to "make check" as their functions are duplicated by other applications.

For help output "-noverbose" should become the default.

David Martin (EMBnet Norway) may visit early next year to discuss CORBA.

Peter will work on generating printable HTML from the EMBOSS application documentation pages. There is a Sanger script already implemented but it will need some customising.

3. Any Other Business

4. Next meeting

Next meeting Monday 6th December, 11:00am, usual place.