EMBOSS: Project Meeting (Fri 20th February 2004)

Attendees

HGMP: Gary Williams, Damian Counsell, Jon Ison, Tim Carver, Lisa Mullan
Lion:
Sanger:
Cambridge Uni:
EBI: Peter Rice
Visitors:

Apologies: Alan Bleasby Thomas Laurent Rodrigo Lopez

Minutes of the last meeting

Minutes of the meeting of 6th February 2004 are here

1. Action points

1.1 From this meeting:

1.2 From previous meetings:

MEME documentation is required (action AJB, 2003-02-21)
EMBOSS Ontology commit (PMR, 2003-11-28)

1.3 No longer required:

2. Software Development

2.1 diffseq

Gary will investigate issues of failing to report differences before and after the overlapping region. These may be simply features of the algorithm, even if the differences are single bases before or after.

2.2 Domainatrix library code

Jon plans to split the domainatrix code into 4 library source files, in either AJAX or NUCLEUS. The files will be specific to structures, domains, database hits and SCOP alignments.

Jon has added an option in contacts to mask nearest-neighbour contacts.

Jon has submitted a paper on cleaned PDB files, and a paper on rocplot. He is now working on domainatrix documentation updates.

2.3 Gotoh algorithm

Damian has commited code in NUCLEUS for the Gotoh alignment method and is comparing results with needle and stretcher.

2.4 acdvalid

Peter has added more checks to acdvalid and updated ACD files.

2.5 cirdna and lindna output

Peter has investigated adding a report format so that these programs can accept output from restrict and other programs for display. This showed that the resulting graphical displays were unusable. The user who originally made the request has now found an alternative solution. Peter will continue to consider display options for report output, but most probably not using these two programs.

3. Documentation & Training

3.1 EBI Industry course

Peter reported his group is again running an EMBOSS/SoapLab/Taverna course as part of the EBI industry Workshop programme. The course is intended to focus more on development issues, but will avoid excessive overlap with the EMBOSS programmers courses.

3.2 EMBOSS Books

Damian would like to meet to discuss the book contracts later in the day. Signed contracts to Damian ASAP please.

3.3 EMBOSS programming course

There are some complications with EMBnet funding for this course, caused by rules limiting funds available to each member.