EMBOSS: Project Meeting (Fri 28th January 2005)


RFCGR/HGMP: Alan Bleasby, Gary Williams,
Sanger: Tim Carver
EBI: Peter Rice, Lisa Mullan

Apologies: Jon Ison,

1. Minutes of the last meeting

Minutes of the meeting of 14th January 2005 are here

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 list.

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" feature format.

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 per plot.

3. Administration

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.

6. AOB

7. Date Of Next Meeting

Next meeting at 9.30 on February 25th, 2005,