EMBOSS: Project Meeting (Mon 9th November 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 2nd November 2009 are here.

2. Maintenance etc.

2.1 Applications

Peter is looking into issues with gene selection in extractfeat.

Mahmut is looking into using wordfinder and supermatcher code for vector sequence detection in short read data. Both applications have been tidied up and new test cases have been committed.

2.2 Libraries

Peter is continuing the cleanup of ajgraph code, looking to remove 4 additional plplot functions which were added in embosswin.

Peter has searched for the original plplot source code for release 4.99j which we first incorporated into EMBOSS. Only binary copies seem to be available on the net now.

2.3 Other

Mahmut is looking into memory handling by SoapLab. The load server classes were increasing, possibly related to permanent space memory. One server had grown and then cleared. The servers will be monitored, waiting for a problem to appear.

Mahmut is looking into an issue with mafft under SoapLab which appears to be related to the use of square brackets in directory names. It has been changed to use relative paths. The documentation on the SoapLab wiki has been updated to improve the wording.

3. New developments

Jon is updating EDAM, working on the field and tool terms. An alpha release is available with 2000 terms and relations for testing and evaluation.

EDAM documentation includes a mission statement, rules and principles, guidelines for developers and guidelines for annotators.

EDAM is being updated to conform to stricter standards, with the aim to produce a first beta release by January 2010.

Jon is adding terms for the data resources in the latest Nucleic Acids Research web services issue, and is using their database category classification. BioMOBY terms will be cross-referenced by EDAM.

A new datatype has been added for "formatted files".

Entities and phenomena are completed. Fields and function terms will be done this week. Te next set will be datatypes and identifiers. The entity terms have attributes, for example "a sequence is an attribute of a macromolecule", "iep is an attribute of a protein". These attributes are used to link bioinformatics and biological datatypes.

Mahmut has updated the EMBRACE Registry tests using 2 versions of the XML::Compile module.

SoapLab services will be annotated as "demo" before the EMBRACE workshop.

Peter has installed Galaxy for testing.

4. Administration

Peter tried to collect past versions of EMBOSS. Releases back to 1.3.1 have been found and retrieved so far.

Alan has a Windows 7 installation with a 1TB disk for testing.

5. Documentation and Training


6. User queries and answers

Alan is looking into an issue with the cbstools EMBASSY package documentation files.

7. AOB

Mahmut and Jon will attend a BioCatalogue annotation Jamboree at the end of the month.

8. Date Of Next Meeting

Peter will be away next Monday at a Next-Generation Sequencing conference.

The next meeting will be on Monday 23rd November.