EMBOSS: Project Meeting (Mon 14th May 2007)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag, Shaun McGlinchey, Martin Senger,
Sanger: `
Apologies: Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 30th April 2007 are here.

2. Software Development

2.1 Libraries

Mahmut is interested in possible XML output formats. This was a low priority in the new grant, but can be covered by work on the EMBRACE project. We need to select suitable formats for sequences, alignments, features and reports.

2.2 Plplot library

Alan is debugging a plplot problem on windows, where the axes are drawn correctly but the plot data is nonsense. This may be related the the known FILE* problem in edialign on windows.

Peter has committed the latest plplot graphics code to CVS.

2.3 Other development

Alan is looking into the conversion details for a contributed fragment assembly package.

Shaun is working on a standard ACD parser, using antler. This will be in the "acdtools" module on the SoapLab CVS server.

Martin asked whether there is a minimum safe abbreviation for qualifier names. Peter will investigate whether a limit can be guaranteed.

Mahmut is working on the SoapLab plugin for Taverna. To get a document/literal interface Peter Ernst's code needed to be extended (it used introspection to convert client objects and had no support for directory inputs). The Taverna team developers are currently working on the WSDL code. There is now a working docuemnt/literal typed interface for the EMBOSS 4 SoapLab server.

Hamish has installed EMBOSS 4.1.0 on the test server, and ran the QA tests. The production server has now moved to release 4.1.0. The old EMBOSS 2.8.0 server is still used, presumably by old Taverna workflows. Mahmut and Martin are looking at JAX-WS.

Martin asked about what the inputs are for the different ways to provide files and sequence data to EMBOSS, including @list, file lists and directories. We need to document what SoapLab expects, and what a Taverna client sends, for each of these.

3. Administration


4. Documentation and Training

4.1 Books

Jon completed the ACD syntax chapter, with autogenerated files included in a template. The existing ACD documentation will need to be reviewed. Background information on sequenc e features is also done.

5. User queries and answers

No new issues.

6. AOB


7. Date Of Next Meeting

May 28th is a public holiday. The next meeting is on Monday 11th June.