EMBOSS: Project Meeting (Mon 22nd February 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 15th February 2010 are here.

2. Maintenance etc.

2.1 Applications

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.

2.2 Libraries


2.3 Other

Mahmut reminded the meeting that a few pedantic warnings remain in jembossctl.c.

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 Jemboss code.

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 fee.

4. Administration

5. Documentation and Training

5.1 Books

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 book.

6. User queries and answers

All outstanding queries put on the Sourceforge tracker.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 1st March.