EMBOSS: Project Meeting (Mon 9th June 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 12th May 2008 are here.

2. Software Development

2.1 Applications

Alan has added an EMBASSY package cbstools to include wrappers for the tools from the CBS group at DTU in Copenhagen. These include signalp and tmhmm which have moved to this package. Another 7 tools have also been wrapped. The EMBASSY version have the prefix "e" added to their names to avoid clashes.

2.2 Libraries

Peter has cleaned up the alignment code to fix a user report that with low gap penalties it was not possible to have two gaps (one in each sequence) without a match in between. This results in calls to the alignment functions being simpler (no need to pass in the matrix). The profile alignments need further checking as the alignment failed to zero the score in the path (for a local alignment) and the correct score was calculated by a separate function working back from the highest score in the path.

Peter will refactor the ajfile functions before the release. This is the one remaining major source file needing cleanup for the developer's guide.

2.2 Jemboss

Mahmut has worked on some high priority fixes.

2.3 SoapLab

Mahmut has discussed SoapLab issues with Martin Senger on his recent visit to EBI. The terminate function has been changed to make sure all functions terminate when called (for example by a timeout).

Mahmut plans to move SoapLab2 to the production server using EMBOSS 5.0.0. This will be upgraded to EMBOSS 6.0.0 in August.

2.4 Other

Jon has been working on design and architecture issues for an object-oriented approach to applications, with feature requirements and use cases.

3. Administration

3.1 Funding

Peter and Alan presented EMBOSS for an EBI internal review on 6th June in preparation for the next round of funding proposals. The review report strongly supports EMBOSS and makes valuable recommendations for future development and funding approaches.

We need to check that logging is in place for downloads (Alan will check with Open Bio) and for SoapLab services.

Peter will draft a new survey for review in 2 weeks.

4. Documentation and Training

4.1 Books

Peter has completed reading through the draft administrator's guide. Two chapters could be added on installation of the MyEmboss EMBASSY package for non-privileged users and installation of mEmboss.

Jon has received the draft of the wEMBOSS chapter, and requested some more text and additional screenshots.

Lisa will send a chapter for the users' guide.

4.2 Training

4.3 Website

Jon is working through the algorithm documentation.

Peter will add documentation for new applications once the updates are completed.

5. User queries and answers

No new issues.

6. AOB

Alan plans to install Fedora 9 on the developer machines.

7. Date Of Next Meeting

The next meeting is on Monday 23rd June.