EMBOSS: Project Meeting (Mon 22nd February 10)
1. Minutes of the last meeting
Minutes of the meeting of 15th February 2010 are
2. Maintenance etc.
Alan has added a new --enable-devextrawarnings configuration
switch and has moved the -Wpadded GCC compiler warning under its
control. The switch has no effect on its own; if specified then the
--enable-devwarnings switch must also be specified. Omission of the
--enable-devextrawarnings switch allows clean compilation of code that
includes third party software such as expat and zlib.
Mahmut reminded the meeting that a few pedantic warnings remain in
Alan and Mahmut have completed the Jemboss work to use
string arrays in its exec handling. Input strings with space
characters are now transferred successfully to EMBOSS. EMBOSS error
outputs and messages are now recorded in job and project directories
using the file name "stderrfile" and are visible to the user.
At some point Mahmut will implement the ProcessBuilder API in the
3. New developments
3.1 BioMart access
Alan has been writing code for the DOM (ajdom.c/h) that will allow
it to read XML files/streams. This will allow more easy manipulation
of third party XML (e.g. from BioMart).
Jon has started adding the EDAM terms mentioned in the previous
meeting. He envisages the work will involve an uninterrupted four
week blitz (and then a further round of clean-up would be needed).
The authors of the Sequence Ontology have provided Jon with SVN access to
all the content and code of their website (e.g. the MISO browser).
Jon has been evaluating ontology editors and OWL. He believes
that issues with the interface and handling of OWL in Protege preclude
its use. The commercial Ontoprise software lacks the required
functionality. He believes the best software solution is TopBraid at
$500 for an academic licence for the 'standard' edition, which has
sufficient features. There is also a 'maestro' version for a higher
5. Documentation and Training
The Admin book is almost ready to go the publishers. The intention is to send
it by the end of the week at the latest. Jon needs to alter the style
sheet to suppress abstracts. Mahmut will have a quick check whether the
recent modifications to the Jemboss installation script need reflecting in
the documentation. Jon will then produce the final version and check for
any large-scale errors.
The EMBOSS team should then give absolute priority to finishing the Users
6. User queries and answers
All outstanding queries put on the Sourceforge tracker.
8. Date Of Next Meeting
The next meeting will be on Monday 1st March.