EMBOSS: Project Meeting (Dec 13th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Val Curwen

1. Matters Arising

Gary collected further contributions for the Xmas kitty.

2. General progress on release 0.0.4

PHYLIP is failing to build with the SGI C compiler. Ian will fix this.

Database indexing with dbiblast, dbiflat and dbigcg is completed. Code to read blast indexed databases will be added soon. Mark will be using these at HGMP to index the full databases for EMBOSS. Peter will document the programs and mail the details to Mark and Alan.

Batch processing is needed. A simple default to running in the background may be good enough, with checks on stdin and stdout.

Val reported that Mark has made progress on the DisGUIse front end for EMBOSS.

Peter has updated Thon's ACD documentation page, and converted it to be HTML as the original version.

Peter has implemented -sask to replace -sprompt as the qualifier option to ask users for the begin and end (and direction for nucleic acid sequences) of a sequence range.

Peter has added -snucleotide and -sprotein to force the sequence type where it cannot reliably be inferred by the program.

Peter has a first draft of the Trends article which he will circulate tomorrow. The deadline for submission is Friday.

Alan has added a recursive file search function ajFileScan which replaces the previous data file search to find, for example, codon usage files.

Peter will be updating the application documentation.

Gary is working on a restriction map display which will reuse some of the code from restrict.

Richard is keen to try GFF feature dumping from selected applications, for example isochore. Most of the code needed should already be in ajfeat.c

There has been a suggestion that HTML output would be useful from applications. After some discussion, it was agreed to postpone any developments for the time being until a clearer picture emerges of how to restructure the writing of output files.

Alan is speaking about EMBOSS at the CCP11 "Bioinformatics Open Software Development" workshop on Friday. About 100 attendees are registered.

3. Any Other Business


4. Next meeting

Next meeting Monday 20th December, 11:00am, usual place.