EMBOSS: Project Meeting (May 17th 1999)


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

1. Matters Arising

2. General progress on release 0.0.4

Peter has mailed the current list of EMBOSS environment variables to Thon.

Peter will work on the ACD command line changes discussed at the March 22nd meeting. These need changes to the ACD internals that will also help with the -help output.

Ian has completed "matcher" (local alignment) and "stretcher" (global alignment) which were requested by David Judge for the Cuban EMBnet course. Ian is now working on alternative dotplot methods to extend the (word based) dotplot application. Dotplot needs to be renamed to avoid a clash with a GCG alias.

Alan has almost completed "seac" for pattern searches through a database.

Sinead has completed "patmatmotifs", "patmatDB" and "prosextract".

Gary had added "wossname" to search application names, functional groups and brief documentation in the ACD files. The debugging applications are reported as such, but need to be cleaned up where they are no longer in use.

Peter noted that the macros in the string library source code clashed with function names and were not in use. It was agreed that they could be deleted.

Peter is working on improving the efficiency of sequence database input by reducing the number of memory and string allocations and deallocations. This is proving problematic because of the number of additional strings with reference counted pointers but should be completed this week.

3. Library documentation

Peter has revised the function and sequence documentation into separate sections by data type. He will draft documentation for these, and for strings, for Jon to review this week.

4. EMBnet Italy

The Italian EMBnet node in Bari would like to send someone in July to work on their utility applications. Some, like "wordup", were in EGCG.

5. EMBnet Australia

The Australian EMBnet node have requested "eclustalw" and the "ephylip" programs as the most needed from EGCG so they can install GCG 10.0 and drop GCG 8.1 and EGCG.

6. Sanger Centre Applications

Peter has promised to include some more Sanger Centre utilities with etandem. They should be easy to convert but care is needed to make sure they can be plug-in replacements in scripts but still support the EMBOSS features.

4. Next meeting

Monday 24th May, usual time and place.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.