EMBOSS: Project Meeting (Fri 5th March 2004)
Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison, Tim Carver, Claude Beazley
Peter Rice, Martin Senger
Minutes of the last meeting
Minutes of the meeting of 20th February 2003 are
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
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.
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
Tom Oinn is implementing LSID code in Taverna, which can be used as a
model for the EMBOSS code.
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.
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
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.
7. Date Of Next Meeting
Next meeting at 9.30 on March 19th, 2004,
Shared Facilities, Hinxton