EMBOSS: Project Meeting (Mon 26th July 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 19th July 2010 are here.

2. Maintenance etc.

2.1 Applications

Peter noted an unreported bu in dbxfasta where the description index has no test for the length of the term. A test has been added to trim the word to the maximum index length both in dbxfasta and in ajindex.c

Mahmut noted that for needle and other alignment applications the number of gaps and total gap length are not reported.

2.2 Libraries

Peter has committed the changes for embossre.equ to be stored and accessed in the REBASE data directory.

Peter has checked the image size definitions in ajgraph.c for PDF and SVG outputs.

2.3 Other

Mahmut has tested a 6.3.0 SoapLab installation with EBI external services. A few minor SoapLab issues were fixed.

Mahmut looked at Jemboss AJAX utilities and classes. We do not use JNI for standalone or client Jemboss (JNI is only used by Jemboss servers using authorisation). We can rename the parent "AjaxUtil" class to "Util" and move the "Ajax" class to the 'server' package.

3. New developments

3.1 Dbx indexing

Peter has reorganized the internal handling of index fields so that they can be extended for OBO format file indexing. Changes are in ajnam.c to allow field-specific resource attributes for the pagesize and cachesize, in ajindex.c to define the default index file names and index types for the common field names, and in embindex.c to use the new defaults when creating new index caches and files for dbx indexing applications.

Peter will install the latest release of EMBL for testing DBX indexing.

3.2 Ensembl

Alan has proposed fixes for problems with Ensembl sequence retrieval. The first is that the regular expression for the Ensembl software version and database fails for EBI's mysql.ebi.ac.uk server as it picks the wrong field for the version and species. This can be corrected with manual parsing, but still fails to find entries. The naming of entries is species-specific, with an ENSG prefix for human genes, and SPAC2f7-1.1 for S. pombe (as an SPO 3-letter prefix). Michael Schuster has been asked about the best way to fix the problem.

The second problem is SQL-related warnings that repository information has been already read.

When entret is used to return the original text, some output should be provided for Ensembl data. We need to decide on useful content to return, perhaps as a FASTA sequence.

4. Administration

Alan has released 6.3.1 with the fixes to file open calls. The EMBASSY packages have been redone with fixes to configure files for the qualifier used for detecting the PDF library used by plplot.

On FreeBSD some further configure changes were required to define the library location.

Alan now has a FreeBSD installation for testing.

5. Documentation and Training

5.1 Books

Jon has sent the final book to the publishers.

Jon has set up new directories and files for the EMBOSS website based on the books.

This will replace the current CVS directory structure, with separate trees for HTML and XML and a new web home page. Each directory will have a readme file explaining the expected contents.

Some additions have been made to the manuals to clean up the develop and user guide appendix with tables of reference information for libraries and applications, now also covering the EMBASSY packages.

The GCG/EMBOSS application comparison table has been added to the user guide appendix

6. User queries and answers

All handled.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 2nd August. Peter will be on vacation.