EMBOSS: Project Meeting (Mon 27th July 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 20th July 2009 are here.

2. Maintenance etc.

2.1 Applications

No changes.

2.2 Libraries

Peter has updated the FASTQ short read input and output code to conform to standards agreed with the Bio-Python and Bio-Perl projects. He has also fixed an issue in reading protein sequences in "genbank" format where multiple sequence input requires the input file to be buffered when re-reading in an alternative format. These changes will be included in the first patch to this release. The code fixes are being tested by Peter Cock of Bio-Python.

2.3 SoapLab

Mahmut has addressed 5 queries.

The run time limit for long jobs (e.g. phylip) will be increased to 10 hours.

Mahmut will announce on the soaplab user list the SoapLab 2.2 typed interface and the update of EBI services to EMBOSS 6.1.0. Both go live on Wednesday 29th. There are few EMBOSS interface changes, mostly in EMBASSY packages.

2.4 Jemboss

Alan and Mahmut fixed issues with compilation of Jemboss with Java 1.4.1 which is the latest version for IRIX. The last Java release on Tru64 is 1.4.2. A Java options problem is currently under investigation.

3. New developments

Peter has added two new versions of entrails called entrailshtml and entrailswiki to write tables of internal data structures and definitions. We will need to also add an entrailsbook application for the book tables, although these are more trivial contents lists. The applications have a -tables qualifier that selects the tables to be written, and defaults to "all".

4. Administration

Alan raised an issue with releasing patches to Jemboss as changes included a new jemboss.jar binary file which is not covered by the current diff/patch procedures. It may be simplest to ask users to download the jemboss.jar file separately for standalone Jemboss installations.

5. Documentation and Training

5.1 Books

Peter has updated the sequence format sections in the books and website. The website was very old, dating from 2002. The book also needed updated references. Format names need to conform to the existing names as these are being agreed with the other Open-Bio projects.

Alan and Mahmut have updated chapters 1-4 of the Admin Guide to cover changes to Jemboss.

Alan has started proofreading the Developers Guide. One of the C examples needs correction. Peter will test all the C examples as he works through the book.

Jon questioned whether some shorter sections (e.g. EMBOSS installation introduction) could be merged into other sections.

Alan noted that some chapters could be loaded into XmlMind while others had problems. Jon suggested this depends on whether the DTD has been included or commented out. This can be addressed by a simple script to (un)comment as needed to create a file that can be reviewed.

Jon has made minor updates to some sections, e.g. removing obsolete EMBASSY packages.

Jon raised the issue of indexing. He has a list of index terms for all 3 books to pass to CUP. It was agreed to postpone any markup of the original docbook files until we know what the requirements are for the publishers. Any markup would need to be preserved in the Word version we supply to them.

Peter will look into generating DocBook XML for the reference guides. As there is a common source for the reference material it can be generated as DocBook, WikiText and HTML without needing to depend on DocBook conversions.

5.2 Website

Peter has copied sequence format example files to the Wiki. Some files need updating, for example EMBL, Genbank and SwissProt to the latest format. Others are EMBOSS example output files and should be updated to the EMBOSS 6.1.0 versions.

The same files will be added to the book CVS in the inc/text directory. They can be included in the User Guide by default. We may later need to edit out the less common files if they take up too much space. They will be kept complete in the online user reference guide.

Mahmut asked whether the include files on the Wiki need to be commented to warn against editing. Peter suggested this is not a major problem as there is no clickable link to them and that adding markup could be difficult as the raw text is used for generating documentation. The application master documents could be marked up, but adding comments in WikiText can result in additional blank lines in the final output.

6. User queries and answers

All done this week.

7. AOB

Peter has mailed the Open-Bio project lists to propose common discussions through the open-bio-l@lists.open-bio.org mailing list. All EMBOSS developers should sign up to this list and join in the discussions which will move there from the biopython and bioperl lists.

8. Date Of Next Meeting

The next meeting will be on Monday 3rd August.