EMBOSS: Project Meeting (Mon 1st March 10)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag

1. Minutes of the last meeting

Minutes of the meeting of 22nd February 2010 are here.

2. Maintenance etc.

2.1 Applications

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.

2.2 Libraries

Peter has fixed PNG output from plplot, and refseqp sequence format which was mis-defined as nucleotide.

2.3 Other

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".

3.2 EDAM

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.

4. Administration

Still no reply in the test server.

Also no reply from Apple.

5. Documentation and Training

5.1 Books

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 is needed.

6. User queries and answers

All outstanding queries put on the Sourceforge tracker.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 8th March.