EMBOSS: Project Meeting (Mon 20th Jun 11)


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

1. Minutes of the last meeting

Minutes of the meeting of 13th June 2011 are here.

2. Maintenance etc.

2.1 Applications

Alan as ported ViennaRNA 2.0 as a release candidate. One applications does not currently work as an output file is written to twice. The configuration uses openmp. Michael has now successfully compiled Vienna 1.7.2 on MacOSX.

Alan has developed wrappers to Clustal Omega as a candidate EMBASSY package.

Alan has utility programs to make release building easier for others. One checks the Makefile in the applications directory to find any missing executables for mEMBOSS. These will be committed to the scripts directory and will be documented, especially for creating new EMBASSY packages.

Alan has committed a bugfix to tcode.

Peter has updated ACD files.

Peter will revise the ACD groups. This may impact SoapLab where the service name includes the name of the group. The group assignments from past releases could be used to maintain the SoapLab service name.

2.2 Libraries


Alan is testing mEMBOSS using the updated qatest.pl script with the -noembassy option.

2.4 SoapLab

2.5 Jemboss

Mahmut is working on a possible change to the Jemboss look and feel.

3. New developments

3.1 Access methods

Mahmut has generated cache files for DAS, dbfetch and wsebeye. The cache generation applications have been renamed and cleaned up to remove additional debugging and testing functions.

Alan is working on a server cache file for BioMart.

Michael has cleaned the header files for Ensembl to format correctly in Emacs. He will add LGPL references, and can add @source headers if appropriate

3.2 New applications

3.3 EDAM

Jon has made EDAM beta 12 available on the NCBO portal. It will soon appear on the EBI Ontology Lookup Service.

Missing relationships have been defined on parent terms. EDAM has a new "identifier" namespace. The "resource" branch has been merged into the "topic" namespace.

Peter has deleted the now obsolete edamissource application as the is_source_of relation defined for resource terms is no longer used.


Peter has validated and updated DRCAT. EDAM term updates have been included. SwissProt cross-reference identifier types are defined. EDAMid lines define EDAM identifier namespace terms and are required for all query identifier types.

4. Administration

Alan requested a code freeze at the end of June to allow time to build and test the release.

Alan corrected the permissions on some source files.

Posters are needed for Vienna.

5. Documentation and Training

Jon reported that the books are now in print at Cambridge University Press.

Peter will update the website with the latest application documentation.

6. User queries and answers

All done.

7. AOB

Michael noted Ensembl now has community forums on SeqAnswers and BioStar.

8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 27th June.