EMBOSS: Project Meeting (Mon 12th July 10)
Peter Rice (at BOSC/ISMB)
1. Minutes of the last meeting
Minutes of the meeting of 21st June 2010 are
2. Maintenance etc.
Alan has updated tfextract to cope with the latest
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
3. New developments
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.
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
5. Documentation and Training
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
6. User queries and answers
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.