EMBOSS: Project Meeting (Mon 11th Jul 11)


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

1. Minutes of the last meeting

Minutes of the meeting of 4th July 2011 are here.

2. Maintenance etc.

2.1 Applications

Alan has updated the GUI attribute to "no" for the dbx and dbi database indexing applications. There is no need to run these under a GUI interface.

Alan noted reports of some administrators erroneously wanting to install the emnu EMBASSY interface under Jemboss. It is unclear why emnu is still in use.

Peter has cleaned up lindna to produce a clear ruler at the top and to correctly calculate overlaps between horizontal text elements. Several users have expressed an interest in using lindna for restriction map displays. Two report formats are available, using commented-out code. "restrict" displays explicitly the 3' and 5' cut sites from restrict output. Report format "draw" displays any features with their feature type.

Peter has defined an EDAM term for each application group, and validated all the 'topic' EDAM relations. All applications now match each of the groups. Several new groups were required, and several applications are now assigned to more appropriate groups.

2.2 Libraries

Peter changed the official default value for the GUI and BATCH ACD application attributes to "yes" in the ajacd code. They were defaulted to "no" but are only used to guide GUI wrappers which all (correctly) assumed the intended default to be "yes".

Mahmut has revised CHADO access to fix a number of minor issues. Feature locations connect to the feature table for the feature ID and the source feature ID, with a warning if a feature is a source features as well as located on another source feature. The source feature is usually a chromosome, contig or scaffold but can involve genes or transcripts. The "is obsolete" attribute in the feature table was set "true" for an unusual use case that caused problems.

An empty output header is fixed. After the release we need to decide whether empty feature headers should be produced to embl, swissprot and GFF3 outputs.


Alan has added PostgreSQL to mEMBOSS. Mahmut noted that both FlyBase and GENEDB use PostgreSQL. Access to InterMine and FlyMine can be investigated after the release.

3. New developments

3.1 EDAM

Jon will regenerate the PURLs for EDAM.

4. Administration

Alan has added two utility applications to build EMBOSS and to test compilation. Both can be committed to the scripts directory. They are especially useful for managing the EMBASSY packages.

Peter proposed delaying the mira EMBASSY package as release 3.4 is already a candidate release. vienna applications are renamed with an 'o' prefix, with the standard names now used in the new vienna2 package for the rewritten Vienna 2 release.

The release notes need to combine the new features listed on the BOSC/ISMB poster with the planned future developments and a note on the EMBOSS books.

5. Documentation and Training

5.1 Website

Jon has a tarball ready for content on the new website.

We can create the website, and then add or redirect any missing URLS cited in the books. We also need to update pages to include the new and extended features in release 6.4.0. Many pages from the existing website are superseded by the books and can be retired.

Peter will update the release and CVS latest documentation when the release is built.

Alan will check whether the .htaccess file needs to be updated on open-bio.

6. User queries and answers

All done.

7. AOB

Jon is in regular contact with a group at the University of Georgia who are working with Galaxy developers to annotate web services and tools using EDAM and importing a subset into the Open Biomedical Investigations (OBI) ontology. This will involve revisions and extensions passed through the OBI committee.

8. Date Of Next Meeting

Next week is the BOSC and ISMB conferences in Vienna. The next EMBOSS meeting will be on Monday 25th July.