EMBOSS: Project Meeting (Mon 11th April 11)
1. Minutes of the last meeting
Minutes of the meeting of 4th April 2011 are
2. Maintenance etc.
Mahmut fixed an issue in dassources and is now searching
for DAS servers that provide parent tags for multiple location
The application now reads more DAS sources, with a fix to HTTP
redirection where the redirect omits the host address.
Peter found and fixed a bug in tables with numeric keys. As
the key is always passed by reference, the key must be created each
time. The bug only affects the new query language - in the other case
where numeric keys are used the key is the address of a page number in
a cache in ajindex.c which is a new address for each cached
page. The fix is to create Const versions of all the numeric key table
constructors (for use by ajindex.c and to ensure keys for
non-const tables are allocated each time they are put into the table.
Mahmut has updated the dbfetch access method to look for
"Error 12 No entries returned" which is implemented by EBI external
services as a 2002 open bioinformatics standard originally proposed by
Mahmut has checked in changes to SoapLab job records.
3. New developments
3.1 Access methods
Alan continues to work on BioMart caches.
Michael continues to work on the updates to support Ensembl
release 61. Ensembl 62 is due for release later this month.
Ensembl uses tables with numeric keys, but passes them by value rather
than by reference so will continue to use its own key and value
3.2 Query language
Peter has implemented functions to merge two tables using the
operators (OR, AND, NOT, EOR) of the new query language. Both tables
are resized to the size of the largest table. Keys at the same hash
array position are compared, and matches are processed. Any unmatched
keys are then processed. Remaining keys in the second table are
deleted at the end.
These functions make the implementation of the query language across
all access methods very easy, with only a few lines of similar code
for each of the 4 possibilities.
Jon has created an identifier branch within EDAM and moved
terms from the data branch where they are clearly identifiers.
Peter will submit to BOSC and to the ISMB technology track.
Jon will submit an EDAM presentation to the Bio-Ontologies SIG.
5. Documentation and Training
Peter circulated the response to the first Annual Report on the
current grant. Most suggestions to update the website and provide
training courses are already in hand, waiting for the books to be
6. User queries and answers
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 18th April. Peter will be away.
The following two Mondays will be public holidays.