EMBOSS: Project Meeting (Apr 19th 1999)


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

1. Matters Arising

Peter and Ian were away last week. There was a brief meeting but no minutes.

2. General progress on release 0.0.4

Several new applications have been added in the past weeks:

Peter demonstrated EMBOSS to the Bioinformatics course in Beijing on April 10th, the first live demonstration of the project to an outside audience.

Alan has increased the default buffer size in ajfile to avoid warning messages. The warnings can stay for now to watch for cases where the buffer is being increased, but can later be commented out.

Alan asked for functions that make a new string, rather than a reference counted copy so that it can be safely edited. Currently there is only ajStrMod which makes a string single-copy. ajStrCopy was proposed as the name for a new function that does this automatically.

Sequence names written to output files need an automatically generated USA so that they can be read again if the file is used as input. There are some USAs that are "read once" which need a default, perhaps a dummy database name of "UNKNOWN:". Examples are reading from applications or from stdin.

HGMP now have purify installed for testing EMBOSS memory leaks.

Gary asked for a new field in the ACD application line, "groups:", to hold a list of functional groups. Peter will add this.

3. Library documentation

Peter will work on the string and sequence functions first.

Some ACD files have fields defined that now have good defaults provided automatically. Peter will document the current recommendations in a mail to the emboss-dev list.

4. Requirements for release 1.0

There is a bioinformatics course at the EMBnet node in Cuba in June. They have no sequence analysis package installed, but will have the Staden package for the course. If EMBOSS can cover the remaining functions in Dave Judge's course book then it could be used for teaching.

Peter will review the course book and list the new applications functions needed.

For applications that use a sequence range there is a need for a function to trim the sequence and return an offset so that numbering is correct. Peter will write one.

5. Next meeting

Monday 26th April, usual time and place.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.