EMBOSS: Project Meeting (Mon 1st March 10)
1. Minutes of the last meeting
Minutes of the meeting of 22nd February 2010 are
2. Maintenance etc.
Peter has fixed showfeat to correctly report after
sorting. The code would be much simpler if child features (exons)
could be stored as a list of features which would automatically sort
with their parent feature.
Peter has fixed PNG output from plplot, and refseqp sequence
format which was mis-defined as nucleotide.
Alan has prepared a patch for the latest release. This includes
patches for Jemboss to handle the wossname command line and to
report messages sent to standard error. Other fixes are
loading clustalw on Windows, and patches from Nicolas Joly. The
patch includes a jemboss.jar binary file which requires a switch on
the diff and makes the patch unusually large (over 1MB).
Mahmut is checking SoapLab issues. There are some unnecessarily
synchronized methods which may be the cause of a timeout in
Taverna. This can be fixed for the local server after the release.
3. New developments
3.1 BioMart access
Alan described how BioMart access works. Separate requests are
made for the attributes, filters, datasets and servers. The database
software version is returned by a configuration request with a very
large result file.Updates to ajdom are needed to read the XML
output. All operations have been tested and run
through valgrind. The configuration results also have
information on the query form for MartView, with (for example) the
bands for each chromosome.
Updated ajdom code is committed. A few functions need to be
added to handle streamed XML data.
Four demonstration application are added to test the DOM parser. They
are built by "make check".
Jon met with James Malone (EBI) to discuss EDAM and the
Software Ontology. There is a general agreement to share definitions,
with EDAM importing data and formats, and SWO importing methods and
terms. This may involve use of OWL format for data exchange.
Still no reply in the test server.
Also no reply from Apple.
5. Documentation and Training
Jon has corrected the presentation and style of the
Administrators book. This is now on Jon's home page and available for
the publishers to download. The abstract sections are replaced with
annotation using the same content. This is in the XML but will not
appear in the finished book text.
Jon is proof reading the Users Guide. Some text rearrangement
6. User queries and answers
All outstanding queries put on the Sourceforge tracker.
8. Date Of Next Meeting
The next meeting will be on Monday 8th March.