EMBOSS: Project Meeting (Mon 8th December 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 24th November 2008 are here.

2. Software Development

2.1 Applications

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 file.

2.2 Libraries

2.3 SoapLab

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 the XSD.

Lists and selections in EMBOSS are complicated if multiple selections are allowed.

Peter will look into generating the Soaplab XSD files directly from ACD.

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 text.

3. Administration

Alan is waiting for a response from Open Bio on the possibility of an EMBOSS wiki.

4. Documentation and Training

4.1 Books

Alan has reviewed the administrator guide and will download the latest version.

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.

4.2 Website

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 distribution.

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.

6. AOB

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.