EMBOSS: Project Meeting (Mon 30th November 09)
1. Minutes of the last meeting
Minutes of the meeting of 23rd November 2009 are
2. Maintenance etc.
Peter is preparing a patch release. This will include a fix for
the fuzzpro problem where the input sequence contains only a
Mahmut has looked into wordmatch using multiple sequences as
inputs. The algorithm first finds word-size perfect matches then
tries to extend them. For multiple sequences this introduces
complications. The first attempt to extend the Nucleus data structure
required too much storage for match locations using the current data
structure. The next attempt will try hash tables.
Peter has updated missing documentation Makefile.am files for
the EMBASSY packages cbstools and mira. These prevented
the installation of the HTML and text documentation for these
Alan noted that HTTP can now retrieve data in 5 forms,
including gzip compression. We currently support complete text and
chunked text (HTTP 1.0 and HTTP 1.1)
Mahmut has fixed the Jemboss install script which was broken in
CVS. The Jemboss contact form on the web site is also broken.
3. New developments
3.1 BioMart access
Alan can successfully retrieve a BioMart registry using HTTP
GET (REST) calls. Code from the SQL prototype interface was reused to
extract the data. An AjPSeqin object was used to support USA queries,
with the detailed USA syntax yet to be decided. A BioMart object is
passed as the Query and Data, with AjPSeqQuery QryData objects.
The host and port are also specified for other methods. Passing in an
object may be better for other methods that using AjPSeqin fields.
The BioMart code is being developed in the ajaxdb directory.
External applications can be added to examine a BioMart registry and
return a list of other registries or datasets, and to examine a
dataset and return lists of fields and attributes.
Mahmut and Jon attended the BioCatalogue annotation
jamboree in Manchester. Jon presented the current status of
EDAM. Mahmut had discussions with the Manchester BioCatalogue
team about auto-generating annotations in SoapLab WSDL using
EDAM. EMBOSS applications will be annotated in SoapLab with EDAM
Mahmut will investigate a SAWSDL plugin for Eclipse.
Alan has installed fedora core 12 on all the EMBOSS
machines. yum appears to have reduced the amount of downloading
needed for updates.
5. Documentation and Training
Alan will update the admin book before starting his holiday.
6. User queries and answers
Peter will attend a meeting of the European Grid Initiative in
Stockholm later this week.
8. Date Of Next Meeting
The next meeting will be on Monday 7th December.