EMBOSS: Project Meeting (Fri 5th March 2004)

Attendees

HGMP: Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison, Tim Carver, Claude Beazley
Lion:
Sanger:
Cambridge Uni: Sylvia Martinelli
EBI: Peter Rice, Martin Senger
Visitors:

Apologies: Rodrigo Lopez Tom Oinn Thomas Laurent

Minutes of the last meeting

Minutes of the meeting of 20th February 2003 are here

1. Action points

1.1 From this meeting:

1.2 From previous meetings:


MEME documentation is required (action AJB, 2003-02-21)
EMBOSS Ontology commit (PMR, 2003-11-28)

1.3 No longer required:

2. Software Development

2.1 acdvalid

Peter has added acdvalid tests for the "knowntype" attributes of strings and data files. There are also tests for complex functions calculating the values of the "standadr" and "additional" attributes. In most cases these have been resolved by replacing "boolean" datatypes with "toggle" datatypes which interface builders can check separately.

2.2 Domainatrix library code

Jon continues to reorganise and clean up the protein stricture and domain library code. Code is moved to nucleus, functions are defined as static where not globally used. Separate source files aer included for PDB parsing, basic data structures and CATH/SCOP domain data. There is also code for database hits, using a "light" sequence object, and some old alignment code for structural families.

2.3 ajfile

Peter has corrected ajfile.c for buffered external processes, but has made other changes so this will be left foer a future 2.9.0 release and can be patched for 2.8.0 for those users who use external applications to access databases.

2.4 Directory objects

The AjPDir directory objects need some code to handle wildcards and exclusion lists, for example to support the cutgextract file specifications through associated qualifiers.

2.5 Life Science Identifiers (LSID)

Peter plans to implement LSIDs as an extension to the USA syntax. Tom Oinn is implementing LSID code in Taverna, which can be used as a model for the EMBOSS code.

2.6 Integration

Claude plans to drop CORBA and Globus, and to work with Taverna and myGrid on EMBOSS intergration for the remainder of the year. This will be the subject of a separate meeting next week.

3. Documentation & Training

3.1 Cambridge user courses

Sylvia has run two follow-up courses on EMBOSS after David Judge's sequence analysis courses (which are still covering only GCG and some parts of Staden). The course includes the command line ijterface, plus Jemboss, W2H and the Staden SPIN interface.

3.2 Osaka

Peter gave a talk in a workshop on DataGrids in Osaka this week. Several other speakers had used EMBOSS and built workflow prototypes. All were most impressed by Taverna and planned to investigate it further.

4. Administration

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

The list will now be maintained on SourceForge. Gary has committed the current list of bugs, features and requests.

6. AOB

7. Date Of Next Meeting

Next meeting at 9.30 on March 19th, 2004, Shared Facilities, Hinxton