EMBOSS: Project Meeting (Mon 11th January 10)
1. Minutes of the last meeting
Minutes of the meeting of 4th January 2010 are
2. Maintenance etc.
Peter has added examples and QA tests for needleall.
Documentation updates from the Wiki have been included in the release
documentation and committed to CVS.
Peter has updated the release number and date for the QA tests
and generated new example outputs.
Mahmut has added statistical information to support alternative
alignment formats in wordmatch
Peter is working on BAM sequence format hoping to get something
completed in time for the release. BAM files can be indexed but for
now EMBOSS will aim to read all sequence data. There are issues with
the data types defined in the samtools code.
Peter has added refseqp protein sequence input format.
Peter has completed definitions for all external
applications. These are defined in ACD files in the "application"
section. All binary files must exist and be reachable. The programs
are invoked using a call to the full path identified during ACD
Mahmut is testing a new Jemboss install script, with help from
a user. Java files were updated over the weekend. Makefiles will go in
Mahmut plans to look into SAWSDL annotation after the release
3. New developments
3.1 BioMart access
Jon has cleaned up 300 comments from the EDAM conversion and
added missing synonyms (e.g. from BioMOBY and MIRIAM). About 30
protein structure terms have been added from PDBML. More are needed
from the wrappers for What If.
For the EDAM workshop later this week, we need to decide on a format
for the ontology to be returned by a URN (e.g. a PURL reference). For
future work it would be helpful to include some deleted terms in the
Jon has updated the list of proposed applications on the Wiki,
and details of planning over the next 6 months to the July release.
Peter will consider dates for an SAB meeting.
5. Documentation and Training
Postponed until the release is completed on Friday.
6. User queries and answers
8. Date Of Next Meeting
The next meeting will be on Monday 18th January.