EMBOSS: Project Meeting (Mon 27th June 2006)


EBI: Peter Rice, Jon Ison, Alan Bleasby, Mahmut Uludag, Shaun McGlinchey
Apologies: Tim Carver, Rodrigo Lopez, Lisa Mullan

1. Minutes of the last meeting

Minutes of the meeting of 12th June 2006 are here.

2. Software Development

2.1 DOM Library

Alan has resumed work on the DOM library. The first tests worked. Code is still uncommented. The library uses XML approved commands to build an XML file in memory and the write it out. The ajdom code will be in the release but not used in any applications at this stage.

2.2 Other development

Peter met with Henrikki Almusa in Helsinki. We had an discussion ling into the evening about code submissions to EMBOSS and the plans Henrikki and Christoph Roos at Medicel have to use EMBOSS. Henrikki's pattern list code has been implemented with some changes (splitting patterns and regular expressions into separate data types).

Clemens Broger of Roche has contributed an extension to iep to allow users to specify disulphide bridges and modified (uncharged) lysines.

Peter has added support for pyrrolysine, which now has an approved amino acid code of 'O'. This means that every alphabetic character is now valid in a protein sequence. At the same time 'J' (Leucine or Isoleucine as they have the same molecular weight) has also been implemented as an ambiguity code.

2.3 Other development

Peter has patched release 3.0.0 for support of the new embl87 ID line. The code is under test, and will be released on the public FTP server.

Alan is considering alternative ways to supply patches.

Jon is working with Mike on a contact-based double dynamic programming alghorithm with clustering to identify coinserved residue contacts in a protein family of arbitrary size with a scoring scheme based on the number and conservation of contacts.

Jon's ACD parser design is progressing. Ideally it will use acdpretty versions of all files to simplify parsing. This is generally the recommended approach for any ACD parser. Although files for the release should be run through acdpretty before distribution the parser will need to cope with updates in between releases.

Shaun is using code from Peter Ernst at DKFZ in Heidelberg as an XML schema for all the EMBOSS data types. The aim is to use this as a reference in WSDL files. Initial tests are using water, which has a suitable level of complexity in its ACD file. With luck, SoapLab2 will be able to share the schema.

Mahmut has reviewed the changes between 2.8.0 (the last SoapLab release) and 4.0.0 using entrails output. There are 24 changed types, 50 new attributes, and 10 new ACD types.

3. Administration

3.1 Release 4.0.0

Peter asked about the best way to implement test databases for 4.0.0. it was decided that we could keep the old EMBL format data for now, as we will lose all the IDs that we know and love as examples. We can work on cleaner examples, perhaps by saving them as .embl files in the test/data directory, after the release.

Jon has tested ememe and emast and completed their documentation as the new "memenew" embassy package. The previous version (the meme embassy package) will be dropped in the release, just as we did with phylip in 3.0.0. memenew will be classed as a beta release.

Alan will need time to modify Jemboss including using the new documentation hierarchy on sourceforge. Peter will copy HTML files to the 4.0 directory ahead of the release for use in Jemboss testing.

Outstanding requests are to be reviewed by Thursday.

3.2 Binary releases

Alan has had requests for liveCD distributions. These are currently available from Bela Tiwari in Oxford. Jon and Peter will contact Bela and ask whether she would mind us taking on some of the work.

4. Documentation and Training

4.1 Website updates

Jon has updated the website, fixing broken links, updating the top level pages, and updating details of EMBOSS interfaces. He has also added details of mirrors of documentation and distributions.

There is a new applications section for suggested new programs.

The home page now links to sourceforge to show the tracker lists.

5. User queries and answers

The list was reviewed. Most had already been resolved.

6. AOB

Alan has fixed boot message issues and CD mounting on the new workstations.

7. Date Of Next Meeting

Next meeting is on Monday 8th June. Back to the normal routine. This will be the last meeting before the release.