EMBOSS: Project Meeting (Mon 26th Sep 11)


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

1. Minutes of the last meeting

The meeting on 19th September 2011 was cancelled. Minutes of the meeting of 12th September 2011 are here.

2. Maintenance etc.

2.1 Applications

Peter has fixed bugs in the reporting by diffseq of insertions in he first sequence. The reported positions were corrupted by a change in EMBOSS 6.0.1 which reverses features where the start is grater than the end, but this should be true for a feature "between" two bases. A new feature constructor preserves this relationship.

2.2 Libraries

Peter has implemented the proposed changes to header files on the delelopers Wiki. ALl header files now have an @include block which describes the LGPL license and includes RCS tags for CVS to report the date, version and author of the latest version of each header file. files.

Peter has moved all deprecated functions to the ends of the source files, and enclosed them in #ifdef blocks. One block is for functions used in the book text from release 6.2.0,the main block is for all other deprecated functions. New configure options determine whether the book or all deprecated functions are included. By default they are all currently ignored.

2.3 Configuration

2.4 Other

3. New developments

3.1 Reference sequences

3.2 Support for interfaces and GUIs

3.3 Data access

4. Administration

5. Documentation and Training

5.1 Web server

Peter would like to replace the home page with a new style that better indicated the documentation, news, mailing lists and other information. BioPython's home page is a good example, but is wiki based.

5.2 Books

Jon has updated the user manual with corrections from the original proofs.

Peter has updated the version numbers and some examples in all 3 books so that the web pages and original XML match release 6.4.0.

For the book text Peter suggested we should use names for the pages rather than chapter and section so that we can link permanently to, for example, functions handling translations.

6. User queries and answers

All done.

Peter is working through the remaining items on the bug tracker list. Most were already resolved. None were serious bugs. Less than 20 items remain.

7. AOB


8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 8th August.