EMBOSS: Project Meeting (Tue 2nd May 2006)


EBI: Peter Rice, Jon Ison, Alan Bleasby, Mahmut Uludag, Shaun McGlinchey, Syed Haider
Sanger: Tim Carver
Apologies: Rodrigo Lopez, Lisa Mullan

1. Minutes of the last meeting

Minutes of the meeting of 6th March 2006 are here.

2. Software Development

2.1 Progress since last meeting

Alan is making progress in integrating thedomc library into EMBOSS. Current work is on the event processing stage. The library should be ready to use at the end of May.

Jon has fixed a bug in palindrome (reporting large sequence positions) and a big in fprotdist.

Peter has completed a cleanup of all applications so that memory is freed before exit. Valgrind reports no memory still allocated for all except the database indexing programs and for a few data access methods where some minor cleanup is needed. This includes a reset function to restore the internal state of ACD processing and allow embInit to be called again. Jon and Mahmut asked whether it would be possible to create master server to invoke EMBOSS applications as function calls. Peter and Alan commented that this is possible in principle but would fail when a fatal error is encountered. One reason for the request was to cover cases where an application could rnu on one sequence or a set of sequences, to direct interfaces such as Taverna to run eiher one call for all sequences, or one instance for all sequences. Peter suggested an ACD attribute for seqall input to allow servers such as SoapLab to indicate a preference.

2.2 Code cleanup

Jon has completed a first pass of redefining names and parameters for general AJAX functions. Peter will implement these and will work through the sequence and feature processing functions.


Alan is hoping to support a native windows build of EMBOSS from release 4.0.0. This is requested by SciTegic for the Windows version of their Pipeline Pilot product whcih curently is limited to EMBOSS 2.10.0, the last release for which Andre Blavier had produced EMBOSSWIN.

Peter met Andre Blavier recently and discussed future support for EMBOSSWIN. Andre is happy to help the EMBOSS team to generate a windows build. We expect some issues with system calls which were a problem in past EMBOSSWIN builds and have changed in EMBOSS since 2.10.0. We also expect some problems with limits on heap space allocation in Windows.

Support for a Windows build would allow windows clients to be cretaed, including a native Windows Jemboss client. Tim is interested in investigating this.

3. Administration

3.1 Funding

The BBSRC funding has been announced in an EBI press release and announced to the EMBOSS mailing lists. Peter gave an interview to BioInform which appeared this week, with supportive comments from Nigel Brown of BBSRC.

Peter will circulate suggestions for future partnerships and contact prospective partners with a view to further funding applications.

3.2 Release 4.0.0

The release date for 4.0.0 will be the traditional 15th July.

The release should include fixes for all bug reports on sourceforge and implementation of major feature requests. Peter noted that any features that make a significant impact on the content of the EMBOSS books (see 4.2) need to be in the release to avoid making the books out of date too soon after they first appear.

Features agreed at the meeting included:

Peter will start a discussion on the emboss-dev mailing list about these and other features.

4. Documentation & Training

4.1 Developer training course

Jon reported on the developer training course which was held on April 18th-20th. A dozen attendees included many from the Hinxton Campus, plus some from the North East and one from industry in Germany. Peter has had preliminary discussions on funding for a course elsewhere in the UK in the autumn (after release 4.0.0 and the draft books are completed). Peter reported that the EBI industry programme is running an EJBOSS workshop for the inductry programe members on May 21st-22nd. This will cover EMBOSS third party application integration, creating EMBOSS interfaces and wrappers, and future core EMBOSS requirements for users in industry.

4.2 Books

Alan and Peter had a meeting last week with Cambridge University Press to update them on the progress of the EMBOSS books. It was agreed that the books would avouid the use of colour illustrations so that many mall print runs could be made. This allows rapid updating of the books for new EMBOSS releases. The text for the books needs to be completed by the autumn.

Alan has made changes to the configuration files for the administration/installation book. Jon will work on demonstration applications for the core AJAX library function groups, and will work through the function documentation looking for any errors or omissions in the function descriptions. Together with the code cleanup (see 2.2) these are the main requirements for the programmers guide.

Jon Tim and Lisa will review the current status of the user book.

4.3 Website updates

Navigation of the application pages is dificult in their current state.

Peter will generate new pages for all applications with navigation between the current CVS and last release versions. A simple apps page is still needed for other application-related pages but the /apps/ URL could be made to point to the current CVS application documentation if this can then link to the 3.0.0 release documentation and other applications pages in the headers.

5. User queries and answers

6. AOB

7. Date Of Next Meeting

Next meeting is again postponed to a Tuesday, 16th May.