EMBOSS: Project Meeting (Mon 2nd March 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 16th February 2009 are here.

2. Software Development

2.1 Applications

2.2 Libraries

Peter has corrected GFF sequence output to use GFF3. Release 6.0.0 included a fix to use only GFF2 sequence output for proteins while the internals were fully tested and updated. This was still in place so that features were in GFF3 but protein sequences were using GFF2 sequence and feature syntax.

Peter has updated the protein feature internals to improve the display of non-standard features in DASGFF output. Updated code and QA tests have been committed.

2.3 SoapLab

Mahmut attended a Taverna workshop in Manchester and aims to update the SoapLab plugin for Taverna.

Mahmut has updated the EMBRACE wiki with EMBOSS 6.0 SoapLab typed services. There have been issues with the typed service WSDL files as they import XSD definitions. Perl clients do not recognize the import definition. Other clients (e.g. taverna) do understand imports but have other problems. The WSDL style will change to include the XSD. This will also make it easier to generate the WSDL with acdxsd.

Results types are extended in WSDL for the Run and RunAndWaitFor methods. Extensions will be avoided so that Taverna can use typed service WSDL files.

Alan suggested checking the EMBRACE technology recommendations for standard service names. Alternative names may be needed to make SoapLab fully compliant.

The SoapLab server was restarted 4 weeks ago (to implement typed services) and has served over 1 million HTTP requests (including Taverna client startups). No hanging threads were seen.

Mahmut has added DAS services for nucleotide sequences. There is now a total of 14 EMBOSS DAS services. Dasty was used for testing. The services have now been run under the Ensembl client, using DbFetch to retrieve data from Ensembl Gene and Ensembl Transcript to retain Ensembl identifiers in the DAS output. Some display issues remain to be resolved.

Mahmut and Peter will attend a DAS workshop next week.

2.4 Other

Peter has added new entries to the SwissProt test database. The existing entries will also be updated to the latest SwissProt format.

Alan noted that when making changes anything that affects the revised book text needs to be noted and checked.

Mahmut has been in contact with the EMBRACE registry team with regard to a programmatic API for service registration.

3. Administration

4. Documentation and Training

4.1 Books

Alan has completed revisions of the administrator's and user's guides for contents, grammar and readability. Peter also needs to check the technical content, especially one chapter on ACD qualifiers, and to provide example files for each data format. Each example file will be included in QA testing.

A printed copy will be needed to make decisions on content, appendices and sections to be excluded from the final versions.

4.2 Website

Alan will work on setting up the new EMBOSS wiki at OpenBio.

Peter has located the original TeX file for the tutorial and will update the examples to use accession numbers and check for changes to outputs.

5. User queries and answers

No new items

6. AOB


7. Date Of Next Meeting

The next meeting is on Monday 16th March. The 30th March meeting will be in the downstairs meeting room by the new training facility.