EMBOSS: Project Meeting (Mon 15th September 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 1st September 2008 are here.

2. Software Development

2.1 Applications

Peter has completed profile improvements to the dbx indexing applications. The run times are no longer sensitive to cache sizes. The most recent change was to reduce I/O by writing pages only when they are removed from the write cache. In 6.0.0 pages were written when the lock bits were cleared.

2.2 Libraries

Alan has written the remaining dbx indexing code to delete from first and second level trees.

2.3 SoapLab

Mahmut has almost completed the migration of web services to production tomcat machines. The test suite passed all tests. Some EMBASSY applications need to be installed by External Services. When ready, links will be switched so that the www.ebi.ac.uk/soaplab address goes to the new services.

Some users of the SoapLab1 derived services remain. Mahmut is looking into providing a message in place of "404 not found" for attempts to use the derived services.

Some EMBASSY applications use directory inputs, for example the MIRA fragment assembly applications. These are passed as lists of files in SoapLab. There is a maximum time limit on SoapLab2 jobs which may catch large mira assembly runs. We can monitor these to check for major users.

The Spinet web interface to SoapLab2 does not yet allow file list input.

3. Administration

Alan reported that Fedora updates are now working again. Kernel updates are on hold until the graphics drivers are available.

4. Documentation and Training

4.1 Books

Jon has completed the markup of Lisa's chapter. Peter to complete reviewing the developer's manual and return to Jon. Some content needs trimming and some extra text is needed.

4.2 Website

Sourceforge announced they will be moving all websites later this week.

4.3 Publications

Jon has completed a first draft of the EMBOSS papers and is working on two papers from Mike's thesis project.

5. User queries and answers

No new issues.

6. AOB

No issues

7. Date Of Next Meeting

The next meeting is on Monday 29th September