EMBOSS: Project Meeting (Mon 11th January 10)


EBI: Peter Rice, Jon Ison, Mahmut Uludag
Apologies: Alan Bleasby

1. Minutes of the last meeting

Minutes of the meeting of 4th January 2010 are here.

2. Maintenance etc.

2.1 Applications

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

2.2 Libraries

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 processing.

2.3 Other

Mahmut is testing a new Jemboss install script, with help from a user. Java files were updated over the weekend. Makefiles will go in next.

Mahmut plans to look into SAWSDL annotation after the release is completed.

3. New developments

3.1 BioMart access


3.2 EDAM

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 ontology.

3.3 Other

Jon has updated the list of proposed applications on the Wiki, and details of planning over the next 6 months to the July release.

4. Administration

Peter will consider dates for an SAB meeting.

5. Documentation and Training

5.1 Books

Postponed until the release is completed on Friday.

6. User queries and answers

None new.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 18th January.