EMBOSS: Project Meeting (Mon 28th April 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 31st March 2008 are here.

2. Software Development

2.1 Applications

Peter has committed the update of the PHYLIPNEW EMBASSY package to include all the changes up to release 3.67. PHYLIP is now up to date. Some applications now produce different results - these were changes in the algorithms of PHYLIP.

Peter has updated the QA tests for the ViennaRNA EMBASSY package. Some application results have changed in the latest Vienna version. The EMBASSY results agree with the latest ViennaRNA native release.

Peter has fixed a bug in wordmatch where overlapping matches were sometimes incorrectly excluded.

Peter has fixed a bug in seqmatchall reporting alignment positions.

2.2 Libraries

Peter has removed selex format from the automatically detected set as bad input files could be read as selex format - for example a user report that EMBOSS alignment output was misread as selex format sequence data.

2.3 SoapLab

Mahmut presented SoapLab at the EMBRACE project annual meeting in Heidelberg.

2.4 Other

Jon is working on Java J2EE and SWING and researching a project to apply these to wrapping and providing a GUI for new applications.

3. Administration

3.1 Patch to 5.0.0

The fixes for wordmatch and seqmatchall should be put on the FTP server.

3.2 Funding

4. Documentation and Training

4.1 Books

Alan has completed reading through the draft copies and passed them on to Peter. Some examples are not working as expected and need some code work. Example outputs need to be generated.

Jon has passed draft copies to the technical staff at the publisher.

Jon has edited the book XML for consistency and use of markup. The XML uses a subset of a DocBook schema but not a subschema so we cannot validate automatically that only a limited subset was used. Revised markup includes command line session prompts, title capitalisation, program listings, screen excerpts and list types. Corrections have been made to the use of DTD, XML entities and Xinclude for the modular structure and for validation over each book in XMLMind.

A new XMLMind version supporting DocBook 5.0 is now available. This will be used to revalidate the documents once corrections have been completed.

Alan noted some issues with wrapping code examples and long command lines. These could be controlled through XMLMind.

The wEMBOSS developers will contribute a chapter. Other contributions are not yet confirmed.

Jon has a comprehensive "to do" list for the books and website.

4.2 Training

4.3 Website

Jon will update the templates directory to standardise the application documentation subsections.

Alan suggested retesting the links on the website. Peter has code for this. Stale links for PISE have been fixed. Incorrect citations for eprimer3 have been corrected (the errors were copied from the primer3_core documentation and are fixed in the latest primer3 release).

A user has reported some HTML files missing from the distribution. The Makefile.am files in the doc/html and doc/txt directories need to be checked for completeness. The missing files have been added by hand.

5. User queries and answers

In addition to the fixes reported above, there are issues of support for clustalw2 by emma and matrix names in prophet output.

6. AOB


7. Date Of Next Meeting

The next meeting is on Monday 12th May.