EMBOSS: Project Meeting (Mon 4th September 2006)

Attendees

EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag
Sanger:
Visitors:
Apologies: Shaun McGlinchey, Rodrigo Lopez, Lisa Mullan,

1. Minutes of the last meeting

Minutes of the meeting of 21st August 2006 are here.

2. Software Development

2.1 Graphics library

Alan is adding ajgxml.c to replace the obsolete ajgraphxml.c functions, using giep as an example application.

2.2 Release 4.0.0

Peter has released the fixes and notified the mailing lists.

Hamish McWilliam (EBI External Services) has suggested more improvements, including adding sequence names to CHAOS and other program output. Peter will add these suggestions to the SourceForge feature requests tracker.

2.3 Other development

Alan is looking into a David Bauer proposal for a modified profit application with a new matrix scanning using a threshold score. In this case the matrix has floating point numbers. Integer and floating point matrices are distinct ACD data types.

Mahmut fixed the memory leaks in the AppLab server used internally by the EBI SoapLab EMBOSS services for EMBRACE and myGrid. The leaks were input objects no longer in use. The memory heap size has also been increased. Thread references have been removed. Four archive files have been combined into a single file. The number of open files has been reduced by flagging files so they are only opened when needed. These changes can be checked in when Martin Senger returns.

Mahmut has found the eclipse profiling tool very helpful in working with the SoapLab Java code, with the "basic memory profile" option. Although slow, this gives information on individual object references rather than groups. Jconsole is also useful to show memory use by objects and heap usage.

3. Administration

Alan has provided instructions for generating patch files.

Peter passed on a request from EBI External Services for a CVS branch for releases and fixes.

3.1 RPMs

Ryan Golhar's RPMs for RedHat Enterprise Linux have been put on the EMBOSS FTP server.

4. Documentation and Training

4.1 Books

Jon is working on the book detailed outlines. The text will be produces in Microsoft Word using a simple style.

4.2 Program documentation

Peter is looking into providing better documentation and examples for application options (another request from Hamish McWilliam). One possibility is to add an advanced options page for each application, with text generated by an annotated test case. To save space, selected files could be excluded (for example, repetition of the same input file).

5. User queries and answers

The list was reviewed. Everyone should review the current list at http://sf.net/projects/emboss/ and close those already dealt with. All requests have been assigned (mostly to Peter).

All new issues were considered to be resolved.

6. AOB

7. Date Of Next Meeting

The September 18th meeting is cancelled as Alan and Peter are unavailable. The next meeting is on Monday 2nd October.