EMBOSS: Project Meeting (Fri 20th February 2004)
Gary Williams, Damian Counsell, Jon Ison, Tim Carver, Lisa Mullan
Minutes of the last meeting
Minutes of the meeting of 6th February 2004 are
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
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
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
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.
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 The user who originally made the request has now found an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
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.
5. User queries and answers
Gary's current list reviewed. Most new issues were already answered.
7. Date Of Next Meeting
Next meeting at 9.30 on March 5th, 2004,
Shared Facilities, Hinxton