EMBOSS: Project Meeting (Mon 21st January 08)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag, Martin Senger
Apologies: Shaun McGlinchey, Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 7th January 2008 are here.

2. Software Development

2.1 Applications

Alan has committed the update to ViennaRNA release 1.7. The QA test results have changed and need to be reviewed. Output formats are different and some internal constants are changed.

Alan found and fixed a bug in dbxflat secondary indices (description, keyword and taxonomy) when key sizes are different sizes.

Peter continued to work on profiling dbxflat and the AJAX and NUCLEUS libraries. Alan has added a simple function to insert a single new identifier in the index pages which avoids reading and rewriting.

2.2 Libraries

Peter noted that the tracking of library internals for debug traces - counting allocation and freeing of strings, lists, and other objects - takes a significant part of the profiling time. It was agreed that this could be removed by wrapping it in a #ifdef block and adding an option to configure.in to turn it on only if needed.

Other profiling improvements include maintaining a reusable array for list nodes in ajlist.c and for id strings in ajindex.c

2.3 SoapLab

Mahmut has been working to resolve dependencies in SoapLab and Taverna.The Java alltools library has been moved from SoapLab to Taverna. Some issues need to be resolved with the older Taverna 1.6 release when switching to Soaplab/Axis.

Providing support for Taverna 1.7 upwards in SoapLab2 is an option.

The latest Java 6 update 4 now suports JAXB 2.1 and JAXWS 2.1.

2.4 Other development

3. Administration

3.1 Patch to 5.0.0

Alan has added a patch for the dbxflat but (see above).

Peter has patches for sequence reading to be added.

4. Documentation and Training

4.1 Books

Jon has completed templates for the existing manuals.

For the developers book some contents will need to be reorganised. Parts can be moved to the administrators' guide or be reference material on the website.

Peter will add a short section on defining new ACD types.

The total book size should be about 200-300 pages when formatted.

Jon is also looking into the tools needed to reformat the book text for publication and for the website. XMLmindPro is an option, costing 200 euros. There may be issues with the DocBook version being used.

Lisa will contribute the Jemboss user chapter.

4.2 Training

Peter will present a half day tutorial on EMBOSS for users at an EBI course "From sequence to gene: genome resources at the EBI" http://www.ebi.ac.uk/training/handson/course_080305_genes.html from March 5th-7th.

5. User queries and answers

No new issues to report.

6. AOB

Happy birthday to Jon

7. Date Of Next Meeting

The next meeting is on Monday 4th February.