EMBOSS: Project Meeting (Mon 12th July 10)

Attendees

EBI: Alan Bleasby, Jon Ison, Mahmut Uludag
Visitors:
Apologies: Peter Rice (at BOSC/ISMB)

1. Minutes of the last meeting

Minutes of the meeting of 21st June 2010 are here.

2. Maintenance etc.

2.1 Applications

Alan has updated tfextract to cope with the latest transfac release.

2.2 Libraries

Mahmut has improved alignment writing in supermatcher for SAM. A minor bugfix has been applied to ajseqbam.c. PDF and SVG support options have been added to Jemboss. Several Jemboss fixes have been applied.

2.3 Other

3. New developments

3.1 BioMart

Alan has implemented a new 'sql' method for retrieving sequence data from networked MySQL or PostgreSQL databases or views. Internally the retrieved data is handled similarly to BioMart and therefore 'biomart' is specified as the format.

3.2 EDAM ontology

Jon has finished incorporating replies regarding the database information file. Several hundred were received. He is making the file more human-readable and will then ask contributors to confirm the data. He is looking at also maintaining EDAM in OWL format. This stems from a request that a very small amount of datatype information would usefully be added (XSD type and cardinality). EDAM should really remain semantic but a small amount of datatype information could be incorporated where it aids clarity and SAWSDL production. OBO cannot support this request (Dmitri) as it is purely semantic.

4. Administration

Alan and Mahmut have been testing EMBOSS & Jemboss prior to the July 15th release (6.3.0). Several bugs have been fixed. Alan reported that EMBOSS now compiles on all available platforms. There is nothing currently preventing a release on the scheduled date.

Alan has contacted the Fedora and Debian bundlers informing them of package dependencies they could usefully add i.e. libharu, MySQL and PostgreSQL.

5. Documentation and Training

5.1 Books

Jon reported that the content is now complete. Blurbs and biographies have been provided to C.U.P. It has been checked that all files marked for inclusion actually exist. The navigation documentation has been improved. A small number of tables have been created manually (automatic scripts will be required in subsequent versions).

6. User queries and answers

All handled.

7. AOB

The requirement for a SAP meeting was highlighted, post-release, now that the libraries can support planned applications.

8. Date Of Next Meeting

The next meeting will be on Monday 19th July.