EMBOSS: Project Meeting (Mon 19th July 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 12th July 2010 are here.

2. Maintenance etc.

2.1 Applications

Alan proposed fixing an issue with the restriction analysis applications my moving the embossre.equ equivalences file to the REBASE data directory.

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.

2.2 Libraries

Alan has removed duplicate definitions for PDF and SVG in the ajgraph.c source file.

2.3 Other

Alan has fixed a problem with the options for the PDF graphics library libharu. The configure option name was changed to --with-libhpdf which matches the configure help text.

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.

3. New developments

3.1 Dbxref

Peter has started on code to parse dbxref.dat and to handle the entries as "data resources". Code is needed to search for and return specifically text, html, XML and URL data.

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.

3.2 EDAM

Jon announced that Matus is planning an EDAM and BioXSD workshop in December.

4. Administration

Alan will make a 6.3.1 updated release to fix the file open compile issues mentioned above. The myemboss and myembossdemo EMBASSY packages would remain at 6.3.0 as they are not changed by the update. The updated release will include a correctly places embossre.equ file and the libhdpf configure option fix both described above. Peter will check the PDF and SVG fix preserves the output dimensions which are included in the duplicated definitions.

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.

5. Documentation and Training

5.1 Books

Jon has completed the content for the Developer's Guide, and updated the formatting of the tables. All 3 books have been scanned through again with minor revisions to XML validity and spelling corrections. Chapter summaries are required by prefix handling, and missing summaries have been added

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.

6. User queries and answers

All handled.

7. AOB

Peter attended BOSC and ISMB. The Open Bio projects discussed further collaborative projects and have identified SAM and BAM formats as the next target for a common approach. There is also interest in common ways to handle large alignments of next-generation sequencing data using disk-based data structures, and in common approaches to transformation of sequence positions.

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.

8. Date Of Next Meeting

The next meeting will be on Monday 26th July.