EMBOSS: Project Meeting (Mon 8th June 09)
1. Minutes of the last meeting
Minutes of the meeting of 1st June 2009 are
2. Current release
Peter has corrected a bug in needle reported by a
user. The first 2 residues may be suboptimally aligned. The cause was
a coding change in 6.0.0 to allow a gap in one sequence to be followed
by a gap in the other. This required a change in the way scores were
processed. The second residue was not correctly compared to all
Peter has updated the parser for MEGA sequence format to parse
the MEGA version 4 style title and format lines and comments within
sequences. The MEGA output will conform to the full MEGA standard
rather than the current intermediate format produced by the MEGA fasta
conversion utility which only inserts a title line.
Mahmut had a meeting with Martin Senger to discuss SoapLab. The
next release will be SoapLab 2.2 with the new typed interface as a
beta feature. It was decided that the remaining tasks are to complete
the documentation and to add new typed interface methods to cleanup,
terminate, waitfor, describe and get partial results for the typed
Mahmut has been looking into Jemboss build issues. Alan
will modify the "make dist" commands to avoid error messages on Linux
when removing CVS directories from the distribution tree.
Jon has completed populating the relations in the EDAM
ontology. The EDAM file has passed the validation script
tests. Jon will announce the update to the EMBRACE annotation
3 New developments
Alan is looking into BioPerl interfaces, and needs examples of
BioPerl Ensembl interface scripts. Peter will provide examples
from the recent EBI internal API course. Fedora can install BioPerl
release 1.5.2, the latest stable release. This version will be used as
the model for EMBOSS development. Ensembl interfaces are needed to
support the Ensembl coordinate system as a way to retrieve sequences
Alan will also look into interfaces to Gene Ontology services.
Jon is working through 160 secondary databases on the EMBOSS
Wiki. About half have been checked so far. The data resource providers
have been contacted for information on programmatic access to services
to retrieve plain text, XML or HTML data. For resources linked to
SwissProt the Wiki has a list of URLs taken from the SwissProt user
manual. Some databases have EMBOSS access methods and parsers, or are
available as text through public SRS servers. Some have plain text
retrieval over HTTP, some wrap the text with HTML or with header or footer
sections. The majority have only a pretty HTML view. In some cases the
HTML view is only a top level view of the data, with further HTML
links to more detail. If parsing is complicated, a basic level of
reporting for EMBOSS would be to simply return the URL to these
Peter plans to add code to the sequence and feature parsers to
report known cross-reference information including taxons, GO terms,
gene names, DR lines and features db_xref tags. This could be a simple
application reporting the results as a list file of "dbname:id"
records. Jon suggested tagging these with the semantic type of
the data cross-references from the EDAM EMBRACE ontology. This could
be tagged as comment lines in the list file output. For some specific
types a separate application would allow only one type of
cross-reference to be retrieved, with a typed output file.
Peter is installing a local copy of the BioLegato latest
Alan brought the RAID server in for testing prior to
reinstallation in the machine room. In tests, when emboss7
communicated with the RAID server it caused the RAID controller to
lock up. The symptoms appear when port B of the SCSI adaptor in
emboss7 is connected. A replacement SCSI card is on order.
Alan reported that Fedora 11 (Leonidas) is still due to be
released tomorrow. The libtool scripts in CVS will be updated to the
version of libtool distributed with Fedora 11.
Alan will look into specifications for the new developer
workstations, including a compatible graphics card for Jon's twin
displays. The old workstations can be used as pure XP machines for
5. Documentation and Training
Jon has reconverted the latest updates, and added the recently
announced kemboss to the list of interfaces.
Book licence, copyright and legal notices have been removed.
Peter needs to order the full versions of XMLmind and the converter.
Peter will include a screenshot of an example page in the ISMB poster.
Peter will announce the new EMBOSS funding on the mailing lists
and will update the web site with the new grant number.
6. User queries and answers
All done this week.
Peter will produce a draft poster for ISMB covering especially
the new developments planned under the BBR grant.
8. Date Of Next Meeting
The next meeting will be on Monday 15th June.