EMBOSS: Project Meeting (Mon 3rd August 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 27th July 2009 are here.

2. Maintenance etc.

2.1 Applications

No changes.

2.2 Libraries

No changes.

2.3 SoapLab

Mahmut upgraded the SoapLab server on Thursday with a 5 hour time limit (reduced from the proposed 10 hours). Result directories are purged after 10 hours (24 hours for the previous version). No errors have been reported. Two EMBRACE registry tests were updated to use revised qualifier names. Reports now truncate all input/output file names to the base name.

3. New developments

Peter has continued discussions of FASTQ format with the Bio-Python and Bio-Perl projects. A clear consensus has emerged on how to interpret the various FASTQ formats and possible error conditions.

Discussions on the mailing lists have pointed out that the topali package includes some formats not currently suported by EMBOSS. Jon will add these to the SourceForge tracker.

4. Administration

Peter produced a 1.1 patch with updates to sequence formats and a fix for an problem with the qualifier name for feature files read with sequence data.

Alan noted that there is no good way to add binary files to the patch. Users running standalone Jemboss will need to manually install a new client.jar file.

Mahmut has updated the Jemboss client to better handle "Jemboss server unavailable" error conditions.

Alan proposed making an updated mEMBOSS available later this week.

5. Documentation and Training

5.1 Books

Alan has checked the Developers Guide up to Chapter 5.

Peter has updated the detailed descriptions of formats in the User Guide. The report format example files need updating to provide more biologically useful results than garnier predictions.

Jon has updated the include file references. The file links are relative to the (xml/section) file in which they appear. Paths in the book top levels including specific usernames will need to be updated.

Jon has marked up application names with references to the website for use in the HTML version of the books. These were internal references but are now external as application documentation is too long for the main books and is moved to the Users Reference Manual. Internal references can appear as section numbers or section headings in the book text. External references just refer to another book.

Jon is correcting XML errors reported by XmlMind. All sections documented now have a "todo" remark for completeness, even if they were empty.

Peter is correcting extra quotes in links as they are highlighted in Emacs.

Jon has revised the Preface sections to reflect the current sections.

Jon has generated Word and HTML converted books which can be passed to the publishers for comment, and are very useful for reviewing the complete text. Peter will use the Word versions to run spell checking.

5.2 Website

Peter will ask EBI external services to update the developer EFUNC and EDATA and the release EFUNCREL and EFUNCDATA databases in SRS.

6. User queries and answers

Alan has reported a problem of failed anonymous FTP access to Open-Bio. Only one site has found a problem.

One user has requested new options for the digest application.

One user has requested a PHYLIP format option supporting longer identifiers (PHYLIP is strictly limited to 10 character names). Peter will check whether any changes are planned in the PHYLIP 3.7 alpha release.

7. AOB

Peter will be attending the GMOD meeting in Oxford later this week.

8. Date Of Next Meeting

The next meeting will be on Monday 10th August.