EMBOSS: Project Meeting (Mon 4th January 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 7th December 2009 are here.

2. Maintenance etc.

2.1 Applications

Peter has updated the documentation makefiles for the EMBASSY packages cbstools and mira.

Mahmut noted that documentation is still needed for needleall before the release. These can be built from the existing needle documentation.

Mahmut has updated wordmatch to search for sequence adaptors, with added statistical information. The changes are being tested by a user. Run times are looking good. The adaptor sequences are compared to a FASTQ file. Half the run time is for processing input, and half for the method.

2.2 Libraries

Peter has renamed further functions to meet the coding standards, especially in the graphics source files. Functions should now have standard names in this release for the developers book text.

Peter has committed new sequence formats for genpept refseq and refseqp which were all using the GenBank parser.

2.3 Other

Mahmut noted that the Jemboss server does not return help files as the mechanism has changed. The authorized server code does not check the EMBOSS version number. Code has been copied from the Jemboss server.

Before the release we should check that all updates in 6.1.0 patches are also committed to CVS.

Mahmut has updated jalview in Jemboss.

3. New developments

3.1 EDAM

Jon has added edamclean as a "make check" application to validate the EDAM ontology file. Tests include blank lines and the syntax of synonym definitions.

Jon is considering whether to include Sequence Ontology (SO) terms as synonyms.

4. Administration


5. Documentation and Training

5.1 Books

Peter has completed the cleanup of function names and revised all function names in the Developers book text.

Peter will write scripts to check the "to do" comments in the XML sources, and to check application names are marked up.

Jon will clean up the markup and update style sheets to highlight application names.

6. User queries and answers

None new.

7. AOB

Peter will attend the last day of the EDAM meeting next week.

Peter attend an ENSEMBL workshop on next generation sequencing. There was discussion of quality scores, and the possibility of replacing phred scores with likelihood values for each possible base. We can extend the Accuracy data in a sequence object to handle this, if the core repositories agree to change.

8. Date Of Next Meeting

The next meeting will be on Monday 11th January.