EMBOSS: Project Meeting (Fri 13th March 09)
1. Minutes of the last meeting
Minutes of the meeting of 2nd March 2009 are
This meeting was moved because Peter is away on Monday 16th.
2. Software Development
Peter has modified the feature types used by applications to
define them using terms from the Sequence Ontology. Previous releases
often used the artificial name "hit" which was represented as an
undefined sequence feature. The SO terms produce better results when
they appear in the output, especially in DASGFF for DAS services, and
in GFF3 which is the default feature output. Report outputs are unaffected.
Peter has updated the feature table internals for nucleotide
sequences to implement the changes in the EMBL/GenBank feature table
v8.0. Non-coding RNA features have been rationalised to use a single
ncRNA feature key with a qualifier to identify the ncRNA
type. Sequence Ontology equivalents have been identified for
immunoglobulin features. Only the S_Region had no exact equivalent and
is represented by an artificial internal identifier derived from SO:0000301.
Peter has further updated the DASGFF output to use a unique
feature identifier. This was required to correctly display results in
the Ensembl browser.
Peter will investigate the possibilities for displaying
sequence-based graphical output in DAS clients.
Mahmut has corrected some issues with concurrent executions and
threads. Service error reports were generated by the test process
taking longer than the timeout period.
Peter and Mahmut attended a DAS workshop earlier this
week. New features planned for DAS 1.6 (the current version is 1.53E)
will be useful for our EMBOSS-based DAS services
Mahmut will try using the proserver Perl-based DAS
server to replace myDAS java for the EMBOSS DAS services.
Alan has set up the EMBOSS Open-Bio wiki. A small EMBOSS logo
has been generated from the first letter of the standard logo. Word
filtering is in place. Bibliographic references can be linked by
PubMed IDs, etc. Text and images are licensed under GNU FDL and
Anonymous editing is allowed, but can be restricted to users with
accounts. External URLs generate an automatic check. Image uploads are
allowed, preferably as GIF or JPG. The top page is protected from
anonymous editing. Backups are to be done by the Open Bio team. Google
analytics are turned off.
4. Documentation and Training
Jon reported that the CUP technical staff cannot process
DocBook XML directly, and prefer a MS-Word version. Jon will
investigate options for conversion of trial chapters via other
stylesheets (e.g. LateX, PDF) as conversion via HTML can lead to
bloated MS-Word documents. Some mechanism will be needed to import
corrections from CUP.
The Madrid course clashes with other commitments and will have to
move later, possibly June.
5. User queries and answers
No new items
7. Date Of Next Meeting
The next meeting is also in the downstairs meeting room by the new