EMBOSS: Project Meeting (Mon 27th June 2006)
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.
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.
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.
There is a new applications section for suggested new programs.
The home page now links to sourceforge to show the tracker lists.
Next meeting is on Monday 8th June. Back to the normal routine. This will be the last meeting before the release.