EMBOSS: Project Meeting (Mon 1st June 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 19th May 2009 are here.

2. Software Development

2.1 Applications

Peter has completed the update of PHYLIPNEW to have the changes in phylip 3.68. QA tests were passed. The code can now be committed.

2.2 Libraries

Alan has completed and committed the library cleanup. Two minor errors were found and corrected in QA testing. Peter will add coding style tests to the embossdoc script.

Blocks of commented out code could in most cases be removed. The primary authors of each library source file should check and remove any code that is now obsolete.

Peter will implement a fix for the loop caused by closing a forked application that still has output to be read. The wait loop in fileClose can be terminated with a timeout. The file object has the end-of-file attribute set when it is safe to wait for the process to end.

Alan notes that there are calls to ajFatal and ajDie in the library code. Peter will check on ways to remove these so that applications do not suddenly terminate rather than returning an error code.

Peter and Jon will review HTML tags and other uses of angle brackets in function documentation so that they are correctly converted for the book HTML.

Peter has looked into details of MEGA sequence format, as a user reported the currently supported format does not match what MEGA produces. MEGA has a simple format that is produced by its FASTA file converter, and a more complete format which is used when MEGA saves results. EMBOSS will support the more complete format.

2.3 SoapLab

Mahmut has updated the emboss4 branch of the EBI SoapLab services.

A few jobs showed the 2 minute timeout from the RunAndWaitFor method. No other problems were noted.

2.4 New developments

Alan is investigating existing interfaces to Ensembl. For queries to a locally installed Ensembl system we have a code contribution from Michael Schuster. To query a remote Ensembl we can consider implementing the BioPerl API or invoking BioPerl scripts as applications. A third option is to access BioMart but this is a lower priority because our primary goal is to support the Ensembl sequence coordinates system.

Mahmut has joined several next generation sequencing email lists, and attended a meeting at CRI in Cambridge with 30 others.

Jon is looking into reading additional data sources and documening them in the Metadata pages on the wiki.

Peter asked about C libraries to support the SOAP protocol. gsoap was mentioned.

2.5 Other

Alan is still working on issues in libgd not recognizing libpng in other locations. The user with problems is running RedHat Enterprise 5.1.

Jon and Peter have reviewed the EDAM ontology relations. Jon has been adding additional relation data to the existing terms.

3. Administration

The new RAID system disks have arrived. Alan will install them in the RAID box and test. The plan is to define two 3TB devices of 7 and 8 disks and have one spare disk.

Fedora 11 is expected soon. The current release date is Tuesday 9th June.

4. Documentation and Training

4.1 Books

Jon has spellchecked all the books with an evaluation version of XMLmind professional.

Peter will order the full version and the converter.

Jon has tested conversion from DocBook to Word. Entities in the DTD need to have the full path rather than a reference. It is easy to convert the existing documents for this. Not all markup ends up as formatted text in Word, for example applications are not in bold or courier and environment varaibles are also not marked up. This can be fixed by correcting the stylesheet, or if necessary by modifying the markup prior to conversion.

5. User queries and answers

None new.

6. AOB

Peter is back from a visit to Canada. Mark Wilkinson is working on SADI, a semantic web annotation system using the BioMOBY registry ontology. Canadian BioMOBY service WSDL files have SAWSDL markup in a style that EMBRACE may be able to adopt.

The BioLegato project is a reimplementation of GDE functionality in Java. Peter has promised to work on conversion of ACD files to GDE config files so that EMBOSS will run under BioLegato as a possible substitute for SeqLab. This will be of interest to former GCG users.

7. Date Of Next Meeting

The next meeting will be on Monday 8th June.