EMBOSS: Project Meeting (Mon 27th December 2006)

Attendees

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

1. Minutes of the last meeting

Minutes of the meeting of 27th November 2006 are here.

2. Software Development

2.1 New applications

Alan has ported dialign 2.2 (as edialign using an existing wEMBOSS ACD file for the commandline. The original program had 10 headers and source files. We may need an include directory in future for porting applications such as this. The ACD file has only a selection of the options in the original program. Output is in fasta and dialign's own format.

Peter is working on the wordfinder application with Tim.

2.2 Graphics library

Alan has completed a third rewrite of the index lineset code to optimize array resizing in memory.

2.3 Profiling

Peter has enabled gcc profiling to optimise reading of EMBL format files for human chromosome 1. Most of the speedup involbves removing regular expressions for sequence, feature and input file parsing. As usual the PCRE library is the rate-limiting factor. Translation has been optimised by using three dimennsional array sizes of 16 rather than 15 for more efficient access.

2.3 Other development

Mahmut reported that a bug in prettyplot (the -alternative option menu) has been fixed. Because of the way SoapLab uses all command line options the prettyplot service was failing. Users have reported no problems - because they never use this option. The SoapLab server has been reconfigured to always use a single CORBA server for AppLab.

3. Administration

Alan is testing under AIX on the IBM loan machine.

Peter and Alan suggested considering a 4.1.0 interim release in the new year.

4. Documentation and Training

4.1 Books

Alan had a meeting with Cambridge University Press. We will meet again for lunch in January.

Jon has converted all existing content to XML. Estimated page counts are 100-200 for the user guide material, 200-300 for the developers book. All will need a thorough read through for duplication and possible updates.

4.2 Web Site

Jingchu has a new web interface WebLab to be added to the interface pages.

5. User queries and answers

The list was reviewed. Everyone should review the current list at 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

EMBOSS Christmas dinner to be arranged in January.

7. Date Of Next Meeting

No meeting on Christmas Day, so the next meeting is on Monday 8th January.

This will be the first meeting of 2007. We move to the meeting room by reception in EBI.