EMBOSS: Project Meeting (Mon 7th January 08)

Attendees

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

1. Minutes of the last meeting

Minutes of the meeting of 10th December 2007 are here.

2. Software Development

2.1 Applications

Alan is updating Vienna from version 1.6 alpha to the latest version (1.7) from Ivo Hofacker.

Alan has identified and fixed a problem in dbxflat and checked it successfully indexes the new EMBL 93 release.

Peter has run gprof on dbxflat and found a 20% speedup by avoiding the use of temporary copies of internal data. Further similar improvements may be possible.

2.2 Libraries

Peter will look into a bug in EMBL/SwissProt incomplete data which is used by the Staden spin interface and is misread as nucleotide.

2.3 SoapLab

Mahmut noted a problem with the caching of older SoapLab jobs and has revised the insertion order and retention values. This also fixed a long-standing issue with AppLab server memory use.

Mahmut has a prototype Taverna 1.7 plugin for SoapLab. The plugin implements special features of SoapLab services.

2.4 Other development

Alan has updated the .emacs template for the latest release of emacs. Major changes were needed as c-mode is superseded by cc-mode. The template will be included in the EMBOSS distribution, along with the contributed ACD editing mode.

3. Administration

3.1 Patch to 5.0.0

Alan and Peter will make a patch to include the bugfixes for psiphi, dbxflat and SwissProt sequence format.

There will be no interim 5.1.0 release as we will freeze code early to prepare the books and this will become 6.0.0

4. Documentation and Training

4.1 Books

Jon will look into converting the DocBook text into a printable version for easier proofreading.

Jon noted the areas in need of most attention are Ajax Handling sections.

4.2 Training

Jon reported that Waqas is now a team leader in Malaysia and is interested in options for EMBOSS training.

5. User queries and answers

Some applications produce no output if there is nothing to report. An example is einverted. These should have some header information provided to avoid empty output files.

Peter had some useful suggestions from EBI external services for USA extensions to allow more detailed database queries.

6. AOB

Happy birthday to Alan

The last meeting was on Tim's birthday. A quick check through the meeting dates for 2008 shows Jon and Peter will also have EMBOSS meetings on their birthdays this year. This happy coincidence depends on 2008 being a leap year.

EMBOSS meetings are now moved to the EBI's new East Wing, in the "Copper Room", which offers a splendid view of Alan's and Jon's old office at HGMP.

7. Date Of Next Meeting

The next meeting is on Monday 21st January.