> EMBOSS: Project Meeting (Monday 24th August 2009)

EMBOSS: Project Meeting (Mon 24th August 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 17th August 2009 are here.

2. Maintenance etc.

2.1 Applications

Mahmut is looking into the possibility of adding end-weighted gaps to the global alignment applications, and the possible need for additional end gap penalty qualifiers.

Mahmut is looking into retention of quality scores and their use in vectorstrip. The current algorithm is not well suited to detecting adaptors in the 3' end of short read data.

2.2 Libraries

Peter has updated function names for the books and will commit code later today.

Peter has profiled reading and writing of fastq-sanger format short read data and identified a number of speedups in I/O processing and avoiding unnecessary string processing. The AjPSeq sequence structure has become bloated. The next code commit will include changes to the initialisation, copying, deletion and use of AjPSeq to make each attribute optional. Some of the more heavyweight attributes (e.g. lists of citations and cross-references) are only relevant for certain input formats.

In collaboration with the other Open-bio projects, most notably BioPython, we now have a set of standard defective FASTQ files to use for testing diagnostic warning and error messages.

2.3 SoapLab

Mahmut is monitoring loaded classes on the SoapLab servers.

3. New developments

Jon will prepare for the EMBRACE ontologies meeting by adding EDAM ontology terms to the ACD files as "relations" attributes.

4. Administration

Peter reported that the new workstations are still on order. Delivery is promised by the end of this month.

Peter has arranged to get together with EBI systems after the next meeting to discuss EMBOSS server options.

Peter has copied standard databases (embl, uniprot, refseq) and some software (galaxy) on to the new RAID disks. Software installations will wait until the new workstations are delivered and installed. Galaxy is a standalone system in python. Data is in /shared/data and packages in /shared/software on RAID.

Peter will set up a doodle poll for possible SAB meeting dates.

5. Documentation and Training

5.1 Books

Peter has refactored function names for several library files (ajCodon, ajRange) and updated the function names for other sections (especially ajfile.c and related source files). The functions in ajgraph.c will need a major effort to clean up their names.

Jon will leave stylesheet editing until we have comments back from the publishers.

5.2 Website


6. User queries and answers

No new items.

7. AOB

Jon and Peter will go to the EMBRACE ontologies meeting in Amsterdam in mid-September.

8. Date Of Next Meeting

The next meeting will be on Monday 24th August. Alan and Jon will be on vacation.