EMBOSS: Project Meeting (Mon 2nd October 2006)


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

1. Minutes of the last meeting

Minutes of the meeting of 4th September 2006 are here.

2. Software Development

2.1 Graphics library

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

Peter is adding graph titles to "graph" plots. The "xygraphs" have a standard layout and titles defined by ACD and the command line. For the general graphs this is considerably more complicated because each plot is set up individually and there are many ways to redraw second and later plots, but does need to be made to work.


Jon is updating the HMMERNEW package top have better defaults for the number of sequences output, and a conditional prompt for the value. The hmmer user guide is referred to by the program documentation and has now been added to CVS.

2.3 Other development

Shaun is working on web service deployment while waiting for a Java version of the dispatcher from Alberto, and attended Paul Weston's Perl refresher couse.

Mahmut has compiled an internal 64 bit EMBOSS installation and resolved a path problem. Profiling showed SoapLab has generally very clean code with only one redundant thread for the lazy fetcher.

Mahmut is now looking at Peter Ernst's SoapLab code and using eclipse to work on typed web services.

Mahmut now has his own local EMBOSS installation for testing SoapLab. Problems with duptype autogeneration and parameter order are fixed. An XSLT issue remains.

3. Administration

3.1 Backups

Alan will change the timings of backups to run during the day so workstations can be powered off overnight. Backups include home directories on local disks.

3.2 RPMs

Jon has put the latest RPMs from Ryan Golhar on the FTP server.

3.3 Proteomics

Jon will discuss possible directions for proteomics applications with two groups who have expressed an interest in using EMBOSS for their work.

3.4 Other

Jon had been looking at FAQamatic documentation for bug tracking.

4. Documentation and Training

4.1 CCP11 training

There have been various discussions about reviving the CCP11 EMBOSS training proposals whose funding was rejected in 2005. These are ongoing.

4.2 Books

Jon has looked through the DocBook tags for version 5 which is just released. Only a small subset would be needed for the books. Tags can be validated and should be OK for the publishers. Conversion options include PDF and RTF (for Word).

DocBook 5 no longer has a DTD. It now uses XMLschema for validation. If we add a new schema (e.g. for ACD) we can include it within the existing namespace.

Jon will create a template for editing. The standard edition XMLmind editor is free and can be recommended for general use. The professional edition may be needed to create PDFs. Cost is about 200. Alan suggested Doxygen as an alternative.

Peter is investigating availability of XMLspy through an agreement with partners in EMBRACE.

Jon proposes a single flat directory structure to maintain the book text, expect possibly for the application documentation. Each file will have a docinfo tag with an abstract for indexing.

The book outlines are complete with titles, major sections and subsections. We need to make sure we know what parts can be completely autogenerated and estimate the number of pages for each of these. The developers book will include selected library modules.

4.3 Loan machines

Alan is trying to get an Intel Mac so that it can be supported and documented in the administration guide. He is also trying to track down contacts for our other loan machines.

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

7. Date Of Next Meeting

Peter and Alan are away in 2 weeks time. The next meeting is on Monday 30th October.