EMBOSS: Project Meeting (Mon 25th January 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 18th January 2010 are here.

2. Maintenance etc.

2.1 Applications

Mahmut reported that on mEMBOSS emma is not correctly launching clustalw because it should check for a .exe extension on the filename in ajFileSysWhich. This is fixed in a patched mEMBOSS.

Alan reported that a new JASPAR database release is available, with a new directory and FTP structure. The developers have been asked to provide advance warning of such changes in future. Alan rewrote jaspextract and jaspscan. The transcription factor binding site matrices now have version numbers as a '.1' suffix. There are many more files in the directory. jaspextract has to use the suffixes to find the file types and create JASP subdirectories. Peter will update the QA tests.

Jon has renamed data structures specific to applications to remove any 'Aj' or 'Emb' prefix.

Alan has updated edamclean to meet the coding standards.

2.2 Libraries

Alan is reviewing shadowed globals and functions, especially for Mac OSX development.

Alan suggested replacing system calls, for example to run "mkdir", with code that can be supported on Windows. Peter offered to work through the system calls replacing them with new functions.

Peter has modified ajFileoutNameDirS to always add a file extension.

Peter has fixed a bug in reading refseqp format protein data.

2.3 Other

Peter noted that a new cygwin release is available. Alan and are now running the new version.

Peter is testing eclipse as a development workbench. The spell checker has been used to update documentation in the source code. There is a very useful function index. To make the views of source files easier, .cvsignore files have been defined.

3. New developments

3.1 BioMart access


3.2 Data formats

Peter is considering options for defining data "servers" as sources of automatically defined databases, including BioMart, SRS, MRS, and directories of flat files.

Peter would like to add new data formats, including completing work on SAM and BAM sequence and alignment data. Further work is needed to provide coverage for non-sequence data resources.

Jon raised issues of maintenance for the database registry. We need to agree a maintenance format, possibly in addition to a distribution format.

3.3 EDAM

Jon has set up a SourceForge project edamontology.sf.net with a tracker for update requests. Documentation has been copied to the new home page. The licence is defined from the OBO Foundry. EMBRACE partners are preparing a paper on the registry with a section on the EDAM ontology.

Jon noted that OBO recommends "intersection_of" as a way to combine two terms.

The ONDEX group at Rothamsted are considering using EDAM internally within ONDEX, but they will need a model of relationships between entities (e.g. 'gene encodes protein').

Jon reported on the Amsterdam workshop on EDAM and BioXSD. A WSDL syntax was agreed and the format for a purl.org reference. We need the registry to define the syntax of the page to which a persistent URL will resolve. As an initial proposal, we could use the OBO format of the term definition.

The coverage of EDAM is good, with very few extra terms needed. Some additions are needed to support BiOXSD annotations.

Heinz Stockinger (SIB) has asked colleagues to review the content of EDAM. SIB will use EDAM to support their website tools.

A beta release of EDAM will be needed soon to provide a stable starting point for users. At this point term identifiers will have to be fixed and terms can no loner be removed. Changes will have to be through obsolete terms and definitions of synonyms.

DTU will organize a workshop on annotation. There will be a follow-up third EDAM meeting in Amsterdam.

EBI has started a series of internal meetings for those interested in ontologies.

3.4 Other

Peter is updating Galaxy to check their EMBOSS interface definitions.

4. Administration

Alan is still waiting for a reply from Apple about loan machines.

Alan will try building on Tom's old mini Mac.

Peter has tested the new Thunderbird 3.0 which seems to be working well now.

5. Documentation and Training

5.1 Books

Jon has heard from the publishers. The section number issues from the sample chapter are OK when working with the whole book. A logo will be needed. Jon hopes to design something soon.

The XML documents reflect the new package structure. Personal email addresses have been removed from the application documentation, replacing them with the emboss-bug address.

EBI training and outreach are interested in trying the book text as online training courses.

The EMBOSS web site will need a new home page and new structure using the book text and Wiki contents.

6. User queries and answers

None new.

7. AOB


8. Date Of Next Meeting

Peter is on vacation for the next 2 weeks. The next meeting will be on Monday 15th February.