EMBOSS: Project Meeting (Mon 15th September 08)
1. Minutes of the last meeting
Minutes of the meeting of 1st September 2008 are
2. Software Development
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.
Alan has written the remaining dbx indexing code to delete from
first and second level trees.
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.
Alan reported that Fedora updates are now working again. Kernel
updates are on hold until the graphics drivers are available.
4. Documentation and Training
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.
Sourceforge announced they will be moving all websites later this week.
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.
7. Date Of Next Meeting
The next meeting is on Monday 29th September