EMBOSS: Project Meeting (Mon 27th Jun 11)


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

1. Minutes of the last meeting

Minutes of the meeting of 20th June 2011 are here.

2. Maintenance etc.

2.1 Applications

Peter has redefined application groups for all EMBOSS and EMBASSY applications. Each group has a defined EDAM term which should be in the ancestry path for at least one topic relation in an ACD file that includes the group. New groups were added for data retrieval, and missing groups added to the hierarchy. A new application ontogetcommon> to return the common ancestor of a list of terms was written specifically to test group definitions.

2.2 Libraries

Peter looked into a report from a user at EBI that concatenated PDB files failed. As this is not valid PDB format it can be treated as a feature, not a bug.


2.4 SoapLab

Mahmut fixed a problem caused by primer3_core compiled under the wrong operating system for LSF.

2.5 Other

Peter reported QA tests and valgrind tests were all working on Linux.

Peter has scripts to update the html and text documentation Makefiles, preserving the current records where no split is needed..

Mahmut is testing Jemboss interfaces and adding a Nimbus look and feel option selectable under "preferences".

3. New developments

3.1 Access methods

Peter has added several OBO ontologies to the release, including the Gene Ontology and Sequence Ontology. They are defined as GO, SO, etc. and have dbxobo index files.

Mahmut has updated CHADO access.

Mahmut can use the dbfetch access method to find cross-reference information. It is possible to retrieve and parse the full entry, or to retrieve reference information.

Michael is preparing cache files for Ensembl data sources.

3.2 New applications

Peter is adding applications to fetch URLs from DRCAT entries where no EMBOSS-parsable format is available. The applications will use definitions from EMBL and SwissProt cross-references to guess at the identifier, or an explicit user definition, where there are several queries to choose from.

Peter has added new applications godef and goname to search the gene ontology in the same way as the equivalent EDAM applications.

New applications could be added to use GO cross-references.

Application edamid is not useful. Retrieval from EDAM by identifier is trivial with ontoget. The edamid application has been deleted.

Peter is adding ACD datatypes for assembly and variation though these will not be used until after the release.

3.3 EDAM


3.5 Other

Peter has added conditional tests to the emboss.default and emboss.standard file parsers. This allows servers dependent on AXIS2C or on SQL to be included only when they were part of the build.

4. Administration

5. Documentation and Training

5.1 Website

The Open Bio cvs view is not working. Anonymous CVS is also occasionally failing.

Peter proposed considering github in future for shared developer access.

Jon will set up a new website on emboss.open-bio.org for testing.

Peter will copy application documentation to the Wiki.

5.2 Books

Copies of the CUP books have arrived and look good.

Peter will take sample copies to ISMB and BOSC.

6. User queries and answers

All done.

7. AOB

Michael suggested following discussions on BioStar and SeqAnswers to catch EMBOSS_related issues.

8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 4th July.