EMBOSS: Project Meeting (Mon 20th July 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 13th July 2009 are here.

2. Maintenance etc.

2.1 Applications

No changes this week while 6.1.0 was released.

2.2 Libraries

No changes this week while 6.1.0 was released.

2.3 SoapLab

Mahmut has fixed a "too many files" problem in the SoapLab servers.

External services have the SoapLab 2.2 generic and typed interfaces working with EMBOSS 6.1.0. "soapaction" was added to the typed interface. Soap::Lite does not work well as a client. XML::Compile is the recommended Perl client interface.

Mahmut will send an announcement to the SoapLab mailing list.

3. New developments

Peter proposed stricter adherence to the GFF3 feature format standard.

Alan commented on the recent mailing list discussions of CUDA and related issues. We should let the developer community explore these. OpenCL is preferable to CUDA (this is also the view of the BioManyCores project). We can look into the Intel ICC compiler support for multiple cores. Alan will investigate the costs.

Alan has continued working on the Ensembl API.

Mahmut is monitoring next-generation sequencing discussions.

Jon described the latest extensions to the database reference file. This now includes detailed decscriptions of URL-based queries with terms for:

About 50 of the 150 cross-reference databases have been annotated. Specific examples of queries are being added to the Wiki though not to the data file. In a few cases URLs support more complex queries, for example adding taxonomy to the query.

Further data resources from the ELIXIR list can be added later. Priority will be given to public data resources funded by BBSRC and to resources cross-referenced by the current set of 150 databases.

Database providers will be asked to comment on the URLs and recommend changes, additional queries to be added and obsolete URLs for removal.

All terms for datatype, format and query term should be from the EDAM ontology, which will be extended as the file is populated. Jon proposed a set of new applications to use the database data file.

query by keyword in the database name and description
display information about all defined data resources.
retrieve all cross-references for a sequence entry. Possibly also new seqxrefxxxx applications for specific types of cross-references data.
information on a biological identifier (EDAM term) as a query term
identify instances for a given identifier, using preprocessing by patterns and brute force querying (as in whichdb) for any resource that may understand the string as an identifier.
return all links (or full entries) for an identifier
retrieve links to data for a specified database, datatype, query term and output format using the database field definitions.

4. Administration

Alan reported the 6.1.0 release was successful for the main package. The 1 week testing period proved just adequate. For Jemboss we need to consider additional QA tests for the GUI (and perhaps for other GUIs) for future releases to avoid the need for manual testing and late changes.

Since the release, Alan reported only a few installation problems were raised and these were X11 configuration issues where the new configure script correctly identified the cause.

Alan will prepare configurations for the new workstations. We do not yet have a delivery date.

5. Documentation and Training

5.1 Books

Peter updated some book files when adding documentation of output formats to the Wiki.

Peter will now concentrate on generating the include files.

Jon will test word and other format conversions.

Alan and Mahmut will review the Jemboss sections.

Jon will add 2 new master documents for a comprehensive programmer reference manual with all the library documentation, and a user reference manual with all the application documentation.

The wEMBOSS section of the user guide has been updated.

The xml/sections files have the latest notes of the reviews needed.

5.2 Website

Peter has added the application and EMBASSY documentation to the Wiki. The EMBASSY documentation needs more work to bring it up to standard both in formatting and in content.

Peter has set up wiki templates for output file formats with the application default format passed to the template. Similar templates can be used where variables are to be passed, for example the package name and version for EMBASSY package installation instructions.

6. User queries and answers

All done this week. Some suggestions have been added to the Wiki and the Sourceforge trackers.

7. AOB

Jon and Peter will attend the proposed EDAM meeting in September.

Jon suggested fully annotating the ACD files with EDAM terms and adding them to the SoapLab ACD parser before the meeting.

8. Date Of Next Meeting

The next meeting will be on Monday 27th July.