EMBOSS: Project Meeting (Mon 8th December 08)
1. Minutes of the last meeting
Minutes of the meeting of 24th November 2008 are
2. Software Development
Alan has updated EMEME and EMAST wrappers to release 4.0.0 of
the original package. ememe uses the original file if it is in
FASTA format, or the temporary FASTA format file which is retained for
reuse by emast. When mast fails with input file problems
emast reports the mast error rather than stopping
prematurely. An ACD function is needed to return the name of the input
Mahmut is working on typed services for SoapLab and is now
using Soaplab2 to execute and retrieve results. The server code only
needed about 200 lines. Type binding code is autogenerated. Some more
tuning work will be needed.
Mahmut is working on common sequence input types for all
services. Typed services have a choice of direct data and USA
attributes, with mandatory use of only one set. The input can be
validated by clients using XSD.
Soaplab allows a URL as a direct data input. This will be included in
Lists and selections in EMBOSS are complicated if multiple selections
Peter will look into generating the Soaplab XSD files directly
The 'run' and 'runAndWaitFor' methods are implemented. Other methods
do not use complex datatypes. Typed services should be available
soon. GFF output can be useful for data integration.
The specifics of using ontologies in XML schema are unclear, for
example how to annotate known types in WSDL and how to include help
Alan is waiting for a response from Open Bio on the possibility
of an EMBOSS wiki.
4. Documentation and Training
Alan has reviewed the administrator guide and will download the
Jon has made changes for XMLMind 4.x. Some checks are needed to
make sure these do not have side effects.
There are some placeholders in the associated qualifier sections where
text needs to be autogenerated as the ACD documentation is updated.
For the function documentation, short descriptions can use the first
paragraph of the description if no alternative is defined. All
descriptions and short descriptions will be reviewed together and
corrected in the source code header comments.
Application descriptions are only in the template HTML file for each
application. They can be more generally useful and could be included
in the ACD file or included from a separate retrievable file in the
5. User queries and answers
Jon will check a reported issue with pdbparse
Peter will patch vectorstrip with the fix already in the CVS code.
7. Date Of Next Meeting
The next meeting is on Monday 5th January, and will start at 10am to
avoid interruptions from the East Wing fire alarm test.