EMBOSS: Project Meeting (Mon 19th July 10)
Alan notes there is a problem in the (unused) newcoils.acd file which had an empty relations: attribute. This has been fixed. There was another (also unused) ACD file with a missing terminating double quote. This was also fixed.
Alan has corrected a problem with opening files using in "create" mode using system functions. A mode argument is required, but only one system reported the problem. Files are opened with mode '644' in an updated 6.3.1 release, provided as on the system that objects this is a build failure. The function is only used by 2 EMBASSY packages (emnu and hmmernew. Peter will check for other cases and fix so that the default user file access modes are used. Peter noted that this problem explained strange results from hmmernew QA tests where an output file could occasionally have no user access.
Mahmut has fixed performance issues in string management in a Jemboss server class when reading XML files.
Jon and Peter have cleaned up the format of dbxref.dat. UniProt have released a new version of their databases file. About 20 new databases have been included. UniProt now have database accession numbers which have been copied to dbxref.dat. Email replies from database contacts have provided 20 new query records. The Link field has been reformatted to provide one record for each link. All EDAM references have been checked and updated.
Alan has added Ubuntu to the list of systems supported.
Alan has created a new emboss.open-bio.org CVS repository for the updated web site design, to be based on the reformatted book text.
Now that the release is out of the way, the latest test system for database indexing can be tested.
The function prototype descriptions have been extended where they were too short.
The AJAX and NUCLEUS library descriptions have been extended
The HTML versions need to be generated again and checked.
Peter reported from his discussions at ISMB that CUP are waiting for example chapters from their typesetters and have announced provisional pricing on fliers that were distributing on their stand.
Peter reported that although the poster sessions at ISMB were very disappointing - held at lunchtime, too brief, and very few people viewing the posters - there was considerable interest in EDAM on the EMBOSS poster and at Matus's technology track demonstration talk.
A Japanese group have designed icons for each EMBOSS applications. They are happy to provide copies.
Peter has joined the samtools mailing list.