EMBOSS: Project Meeting (Mon 3rd March 08)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Shaun McGlinchey,
Apologies: Mahmut Uludag, Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 18th February 2008 are here.

2. Software Development

2.1 Applications

Peter has modified dbxfasta to warn if any unique identifier is truncated. The program will report the first truncated ID, and at the end will report the number of truncated IDs and the maximum ID length parsed from the input database.

The same message should be added to the other indexing programs.

2.2 Libraries

Alan has fixed two problems in the ajindex.c code used by the dbx indexing applications. One was in the locking of secondary root pages, the other in locking non-root pages in the insert functions. The problems appeared for one user when using a large PAGESIZE but only a small CACHESIZE.

Peter noted potential locking problems with code for deleting from an index. The debugging functions can be left in place until index deletion is fully implemented.

2.3 SoapLab

Mahmut has regenerated the EMBRACE Wiki pages. Some EMBASSY application links failed. The pages now use the SoapLab2 client library. Code has been checked into subversion. The EBI soaplab pages are also updated. Martin has suggested a SoapLab page for Wikipedia.

Mahmut will look into replacing SoapLab services with SoapLab2 if the change is transparent to users. Metadata for the catalogue service has some changes.

Migration from emboss 2.8 for the older services can be delayed until after the release of EMBOSS 6.0.0 in the summer, with an automatically generated page to docuemnt differences between the two versions based on existing scripts.

2.4 Other Development

Mahmut attended a DAS (Distributed Annotation System) workshop last week at EBI. There is potential for EMBOSS and Jemboss to work more closely with JalView, and with the WAMSAS project for XML formats.

Lisa is reviewing the list of feature requests for Jemboss.

3. Administration

3.1 Patch to 5.0.0

Peter has copied over the modified source files for sequence reading and Genbank output.

Alan will review the changes and any further ajindex.c fixes and build a patch.

4. Documentation and Training

4.1 Books

Alan has completed reading and annotating the administrators' guide and passed the editors' copy to Peter. Next to be reviewed is the developers' guide.

4.2 Training

Peter will present a half day tutorial on EMBOSS for users at an EBI course "From sequence to gene: genome resources at the EBI" from March 5th-7th. Mahmut will attend and help with the practical session. See http://www.ebi.ac.uk/training/handson/course_080305_genes.html for details.

4.3 Website

Some pages on the website need to be updated, for example the list of support systems. Text from the books can be used once it has been checked.

Jon is reviewing the application documentation. So far he is about half way through.

5. User queries and answers

The dbxfasta problem was fixed (see above). investigate.

6. AOB

Alan noted that it is time to consider funding options. The current grant runs to the end of April next year.

7. Date Of Next Meeting

The next meeting is on Monday 17th March.