EMBOSS: Project Meeting (Mon 8th June 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 1st June 2009 are here.

2. Current release

2.1 Applications

Peter has corrected a bug in needle reported by a user. The first 2 residues may be suboptimally aligned. The cause was a coding change in 6.0.0 to allow a gap in one sequence to be followed by a gap in the other. This required a change in the way scores were processed. The second residue was not correctly compared to all previous gaps.

2.2 Libraries

Peter has updated the parser for MEGA sequence format to parse the MEGA version 4 style title and format lines and comments within sequences. The MEGA output will conform to the full MEGA standard rather than the current intermediate format produced by the MEGA fasta conversion utility which only inserts a title line.

2.3 SoapLab

Mahmut had a meeting with Martin Senger to discuss SoapLab. The next release will be SoapLab 2.2 with the new typed interface as a beta feature. It was decided that the remaining tasks are to complete the documentation and to add new typed interface methods to cleanup, terminate, waitfor, describe and get partial results for the typed SoapLab jobs.

2.4 Other

Mahmut has been looking into Jemboss build issues. Alan will modify the "make dist" commands to avoid error messages on Linux when removing CVS directories from the distribution tree.

Jon has completed populating the relations in the EDAM ontology. The EDAM file has passed the validation script tests. Jon will announce the update to the EMBRACE annotation mailing list.

3 New developments

Alan is looking into BioPerl interfaces, and needs examples of BioPerl Ensembl interface scripts. Peter will provide examples from the recent EBI internal API course. Fedora can install BioPerl release 1.5.2, the latest stable release. This version will be used as the model for EMBOSS development. Ensembl interfaces are needed to support the Ensembl coordinate system as a way to retrieve sequences in EMBOSS.

Alan will also look into interfaces to Gene Ontology services.

Jon is working through 160 secondary databases on the EMBOSS Wiki. About half have been checked so far. The data resource providers have been contacted for information on programmatic access to services to retrieve plain text, XML or HTML data. For resources linked to SwissProt the Wiki has a list of URLs taken from the SwissProt user manual. Some databases have EMBOSS access methods and parsers, or are available as text through public SRS servers. Some have plain text retrieval over HTTP, some wrap the text with HTML or with header or footer sections. The majority have only a pretty HTML view. In some cases the HTML view is only a top level view of the data, with further HTML links to more detail. If parsing is complicated, a basic level of reporting for EMBOSS would be to simply return the URL to these services.

Peter plans to add code to the sequence and feature parsers to report known cross-reference information including taxons, GO terms, gene names, DR lines and features db_xref tags. This could be a simple application reporting the results as a list file of "dbname:id" records. Jon suggested tagging these with the semantic type of the data cross-references from the EDAM EMBRACE ontology. This could be tagged as comment lines in the list file output. For some specific types a separate application would allow only one type of cross-reference to be retrieved, with a typed output file.

Peter is installing a local copy of the BioLegato latest development version.

4. Administration

Alan brought the RAID server in for testing prior to reinstallation in the machine room. In tests, when emboss7 communicated with the RAID server it caused the RAID controller to lock up. The symptoms appear when port B of the SCSI adaptor in emboss7 is connected. A replacement SCSI card is on order.

Alan reported that Fedora 11 (Leonidas) is still due to be released tomorrow. The libtool scripts in CVS will be updated to the version of libtool distributed with Fedora 11.

Alan will look into specifications for the new developer workstations, including a compatible graphics card for Jon's twin displays. The old workstations can be used as pure XP machines for mEMBOSS development.

5. Documentation and Training

5.1 Books

Jon has reconverted the latest updates, and added the recently announced kemboss to the list of interfaces.

Book licence, copyright and legal notices have been removed.

Peter needs to order the full versions of XMLmind and the converter.

Peter will include a screenshot of an example page in the ISMB poster.

5.2 Website

Peter will announce the new EMBOSS funding on the mailing lists and will update the web site with the new grant number.

6. User queries and answers

All done this week.

7. AOB

Peter will produce a draft poster for ISMB covering especially the new developments planned under the BBR grant.

8. Date Of Next Meeting

The next meeting will be on Monday 15th June.