EMBOSS: Project Meeting (Mon 30th November 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 23rd November 2009 are here.

2. Maintenance etc.

2.1 Applications

Peter is preparing a patch release. This will include a fix for the fuzzpro problem where the input sequence contains only a stop codon.

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 packages.

2.2 Libraries

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)

2.3 Other

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.

3.3 Other

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 categories.

Mahmut will investigate a SAWSDL plugin for Eclipse.

4. Administration

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

5.1 Books

Alan will update the admin book before starting his holiday.

6. User queries and answers

None new.

7. AOB

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.