EMBOSS: Project Meeting (Jan 18th 1999)

This was the first of a new series of EMBOSS project meetings.

A group of Hinxton staff actively working on EMBOSS or closely interested in the project met to discuss progress and to consider options for future regular project meetings.


Sanger Centre: Peter Rice, Ian Longden
HGMP: Gary Williams, Alan Bleasby, Sinead O'Leary, Thon de Boer, Mark Faller
EBI: Heikki Lehvaslaiho, Martin Senger (Apologies: Rodrigo Lopez)

1. Introduction

A first full release of EMBOSS is due very soon. PR and IL are cleaning up a few loose ends, mainly documentation and the graphics library. Meanwhile, HGMP are getting up to speed with EMBOSS applications code development. There are clearly a number of areas of interest to be covered by this and future meetings.

At the Sanger Centre, PR and IL are concentrating on the core libraries and applications for EMBOSS, and project coordination.

At HGMP, the applications and user support group is aiming to use EMBOSS to develop software that is better than the packages they currently have available. HGMP also coordinates the UK CCP11 project (AB and MF).

EBI has interest in EMBOSS in the database services and industry groups. Other EBI staff may want to attend future meetings.

Agreed: To meet weekly at 11:00 in the Sanger Centre

Agreed: To invite others in the Cambridge area who might be interested in the project to attend

2. News of the next release

PR and IL described the status of the next release. This will be made available once the graphics library builds automatically on all platforms and some further source code documentation and testing is completed. This is expected to take a couple of days.

The new build procudure follows GNU standards. Users need only unpack the distribution, then run "configure" and "make install".

Developers will find it easier to use the full source code tree which we maintain at the Sanger Centre. This uses automake, libtool and other utilities to simplify adding new applications. Developers update "Makefile.am" files. The utilities create the "configure" script and the makefile automatically.

The current graphics library is PLplot.

PLplot was selected because it is distributed under the GNU Library license. This is critical to allowing third party applications to be included in EMBOSS when they cannot be distributed under the full GNU license. An example of this is the PHYLIP package from Joe Felsenstein.

PR commented that other graphics libraries had been considered. One that remains interesting is the GNU libplot library from the GNU plotutils package but this is currently only under GNU GPL. GNU libplot supports X11, postscript and "GNU MetaFile" among other formats.

Agreed: PR to investigate how best to make the source tree available to HGMP

Agreed: Next meeting will include presentations on the new release

3. Documentation

PR has updated the source code documentation for all AJAX library code. This is now on the Web pages for review.

PR has written an "Introduction for Developers" document to help new application developers to get started. Comments are welcome.

Documentation for applications was discussed. PR would like proposed applications to be documented in detail, using a format proposed by GW on the emboss mailing list. This would serve as a program specification for developers, and be converted into end user documentation when the application is released.

Agreed: To review these pages at the next meeting and to link to the main project pages when approved

Agreed: To review application status and documentation at the next meeting

4. Future issues

HL raised the issue of how to represent features. GW and other are also keen to make this a priority area.

Agreed: EMBOSS should be able to use at least GFF files and the feature table of EMBL/Genbank and SwissProt entries to obtain and exchange feature information

Other packages could be included in EMBOSS. Those under active consideration at present are: PHYLIP, FASTA and WISE.

Joe Felsenstein has given permission for PHYLIP programs to be included in EMBOSS but under their original licenses. PR has converted one program to test feasibility and found few problems.

Bill Pearson has expressed interest in integrating the FASTA programs into EMBOSS, and in possibly maintaining such a version, again under the original license.

The WISE package is GNU licensed already. PR hopes that Ewan Birney will be able to produce and maintain an EMBOSS version.

5. Next meeting

Monday 25th January, Sanger Centre Informatics meeting room.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.