EMBOSS: Project Meeting (Mon 20th Jun 11)
1. Minutes of the last meeting
Minutes of the meeting of 13th June 2011 are
2. Maintenance etc.
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
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
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
Alan is testing mEMBOSS using the updated qatest.pl
script with the -noembassy option.
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
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.
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
Peter will update the website with the latest application
6. User queries and answers
Michael noted Ensembl now has community forums on SeqAnswers
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 27th June.