EMBOSS: Project Meeting (Fri 9th January 2004)


HGMP: Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison
Lion: Thomas Laurent
Cambridge Uni:
EBI: Peter Rice, Tom Oinn

Apologies: Rodrigo Lopez Martin Senger

Minutes of the last meeting

Minutes of the meeting of 12th December 2003 are here

1. Action points

1.1 From this meeting:

1.2 From previous meetings:

MEME documentation is required (action AJB, 2003-02-21)
EMBOSS Ontology commit (PMR, 2003-11-28)
Convert graphics to grout (PMR, 2003-09-19) postponed to 2.9.0

1.3 No longer required:

2. Software Development

2.1 pdbplus - a new application for domainatrix

Jon described pdbplus, now committed to the domainatrix EMBASSY package. This program runs stride for solvent and secondary structure and naccess for solvent accessibility, using clean PDB input data, and producing an annotated structure file as output.

In future this will be merged with domainer and pdbparse.

2.2 Graphics

Alan discussed various options for graphics including openSG (a German library) http://www.opensg.org/, and the Fast Light toolkit (FLTK) http://www.fltk.org/

Peter has started to convert the ajgraph function calls to Hugh's ajgraphxml interface.

2.3 psiphi

Damian has a new program psiphi to add torsion angles to cleaan PDB files.

3. Documentation & Training

3.1 New CVS repository for for EMBOSS books

Damian described the CVS files on On Open-Bio. This has custom Makefiles so that author's can generate human-readable output for each of the books.

Running "make" will generate a file in an html subdirectory in textbook output style, a program listings directory for raw C source files, and an images directory. There is no clear decision yet on a preferred DocBook include method.

"make check" will carry out validation, with reportd that are active in emacs/xemacs

"make tidy" will set indent levels

"make clean" will delete files as usual.

3.2 New Look for EMBOSS Web Pages

Damian asked for feedback on the web page layout distributed a few days ago, which is more compliant with browser standards than the old (formerly Sanger) layout of the current web pages. Tom suggested adding RSS news feeds - these can be maintained as a hand-edited file if there is only a low volume of news.

3.3 Questions for EMBOSS Authors from C.U.P.

Damian outlined options for the EMBOSS books. Tom will be added as an author for sections on workflow.

4. Administration

4.1 Release 2.8.0

Alan reported that the 2.8.0 release went exceptionally smoothly.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. CCP11 Software Steering Committee

Alan reported that there was no news yet on a software steering committee meeting.

9. AOB

Alan is hoping to try an HP-UX/Linux dual boot machine.

10. Date Of Next Meeting

Next meeting at 9.30 on January 23, 2004, Loft Room, Hinxton Hall