EMBOSS: Project Meeting (Fri 9th January 2004)
Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison
Peter Rice, Tom Oinn
Minutes of the last meeting
Minutes of the meeting of 12th December 2003 are
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.
Alan discussed various options for graphics including openSG (a
German library) http://www.opensg.org/, and the Fast Light toolkit
Peter has started to convert the ajgraph function calls to Hugh's
Damian has a new program psiphi to add torsion angles to cleaan
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
"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.
4.1 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
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