EMBOSS: Project Meeting (Mon 9th November 09)
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.
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.
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.
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.
Alan has a Windows 7 installation with a 1TB disk for testing.
The next meeting will be on Monday 23rd November.