EMBOSS: Project Meeting (Fri 28th January 2005)
1. Minutes of the last meeting
Minutes of the meeting of 14th January 2005 are
2. Software Development
2.1 Database indexing
Alan reported that some EMBL entries have very long keywords,
and suggested a maximum length. Searches will be case insensitive - all
text is stored in lower case.
A new resource attribute of "order" defines the number of pointers in
an index page disk block.
2.2 New programs
Peter is looking into updating the "new applications" page on
Sourceforge, including programs submitted to the emboss-submit mailing
2.3 Construct EMBASSY package
Damian has moved his code into a separate EMBASSY package
(called "construct") while it is under development.
2.3 Sequence features
Peter will work through Tim's list of new features - mainly from
the latest EMBL/Genbank feature table document - and update them
EMBOSS feature code.
Some extra features for Sanger could be added to a new "artemis"
2.4 Dot Plots
Lisa noted that dottup and dotmatcher are inconsistent in graph
axis markup. One numbers from one, the other from zero.
2.5 Example output
Peter has updated the QA tests which generate examples for the
sourceforge website and the M documentation. All dates should now be
set to 15th July 2004 at 12 noon (the last release date).
2.6 Start codons in translations
Gary has changed tranalign to use 'M' as the translation of
alternative start codons.
2.7 Jemboss graphics
Tim has editable graphics for half the graphical output
produced under Jemboss (dotplots, cpgplot, etc.) with one extra page
3.1 Release 2.10.0
Due to be released next week. Will fix Java 1.5 issues in Jemboss and
include alignment format and feature table updates.
4. Documentation & Training
Peter will go to Detroit and propose a talk at BOSC, and a
demo and poster at ISMB.
4.2 Purdue Course
Peter and Lisa will visit Purdue University (Indiana) for a
1-week bioinformatics course featuring talks from NCBI and EBI, and
will include a half day workshop on EMBOSS for programmers.
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 February 25th, 2005,