EMBOSS: Project Meeting (May 15th 2000)


Sanger Centre: Peter Rice, Ian Longden
HGMP: Alan Bleasby, Gary Williams, Tim Carver
Apologies: Jon Ison, Val Curwen

1. Matters Arising

2. General progress on release 0.0.4

linplasmid and cirplasmid should be removed - they are replaced by lindna and cirdna.

Peter is working on modifications to output file and sequence range types in ACD.

Using the "-ossingle" qualifier, or implying it with GCG format output, should not create an output file in ACD processing as it is ignored later.

Gary updated fuzztran output formatting.

Peter has completed coding sequence database reading for BLAST formats. This will need further testing next week before being committed. All blast formats are covered (NCBI 1 and 2, DNA and protein, with optional FASTA file to resolve DNA ambiguities) with the exception of the new BLAST 2 multi file format where there are currently no examples at Sanger. However, the EMBOSS EMBLCD/Staden index file format will cope with multiple files and so this can be easily extended.

The ajSeqMakeUsa function has some problems still, for example db:* names, and some list files. Peter will investigate.

Peter is looking into phylogenetics and sequence alignment formats for an alignment database project at EBI. Output is available, and was easy to do. Examples of the formats are needed to make sequence reading work robustly.

Alan has implemented dynamic arrays as AjPInt, AjPInt2d, AjPInt3d (etc.) for integer, long, short, float, and double, with up to 3 dimensions each.

We should aim for a beta 1.0 release as soon as possible. Probably when the documentation updates and sequence reading are in place.

3. Features

4. Graphics

PLPLOT 5.0 is released. Ian will check on the changes, and any impact on the X11 colourmap problem.

5. Documentation

Gary has revised the documentation up to "I". The main changes are adding or extending the description section and describing the output format(s). Extra help text is being added to the ACD files where appropriate for the command line options. Examples where possible will use data from the test databases (TSW etc.)

Links to the EMBASSY applications are not correct on the web pages. Also, EMBASSY applications are not included in the group pages. Peter will investigate.

Val proposed parent and child groups for applications. Gary will change wossname and Peter will look at documentation and library changes.

Peter is writing a web page on the various interface collaborations.

The Sanger documentation pages need to change to be usable at HGMP and to be distributed to other sites. Peter will work on a simplified version without the stylesheets and sidebar.

The ChangeLog file does not include much information on code changes (actually, it is still empty). Peter will make a merged file CvsLog from the CVS logs at Sanger and HGMP.

6. Any Other Business

7. Next meeting

Next meeting on Monday 22nd May, 11:00am, usual place.