EMBOSS: Project Meeting (Mon 7th December 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 30th November 2009 are here.

2. Maintenance etc.

2.1 Applications

Peter has applied various fixes to fuzzpro.

Mahmut continues to look into wordmatch. It will be possible to keep the existing data structures, with a wrapper structure to improve efficiency.

2.2 Libraries

Peter has committed recent changes.

2.3 Other

Alan is looking into Jemboss issues for a user.

Mahmut is patching the Jemboss install script. With a new distribution generated from CVS with "make dist" the new script worked. An ant dependency for a different location is used to test for server results (usually in /tmp/soap/emboss). Without ant the java file needs to be changed and reinstalled. For the release, the ant dependency will be replaced by using a property.

3. New developments

3.1 BioMart access

Alan can now get lists of attributes and filters, and is trying to match them up. The original output had two columns to compare but there were complications. Syed is helping with a patch.

A new parser was needed for tab-separated values with empty fields. This can be merged with the parser used for SAM sequence format.

3.2 EDAM

Jon has imported terms for database categories from ELIXIR and also checked the categories used by Nucleic Acids Research. All ELIXIR survey databases are now represented by EDAM terms. New high level terms and relations/rules were added.

Jon has a small program to update, including updating relation end points. This also checks the syntax of records, and checks for required relations. It is able to edit ID numbers and renumber terms, and is namespace aware when checking for duplicated names.

At the annotation jamboree in Manchester there was clear interest in EDAM and discussions of use cases. There was no prior agreement on how to annotate, so EDAM was especially helpful.

4. Administration

A meeting is scheduled with the EBI systems group to discuss our proposed server configuration.

Alan has set up Syed's old machine (emboss17) as an httpd server. All machines should see /shared/www mounted with an html/ directory. The contents are included in the backup procedures.

The server also has a pure, unadulterated Wiki http://emboss17/wiki where we can register.

5. Documentation and Training

5.1 Books

Alan has updated the AJAX directory stricture in the administrators book.

6. User queries and answers

None new.

7. AOB

Peter will go to an EGI (European Grid Initiative) meeting.

8. Date Of Next Meeting

Monday 14th December is an Ensembl workshop on next-generation sequencing. For the other December dates we will be on vacation. The next meeting will be on Monday 4th January.