EMBOSS: Project Meeting (Fri 24th January 2003)


HGMP: Alan Bleasby, Martin Bishop, Lisa Mullan, Tim Carver, Damian Counsell, Jon Ison, Hugh Morgan, Claude Beazley, Gary Williams
Lion: Thomas Laurent, Bijay Jassal,
EBI: Adam Lowe, Sharmila Pillai, Rodrigo Lopez, Peter Rice

1. Matters Arising

Alan reported that (i) SGI are supplying a 64 but 4-processor m/c for EMBOSS. (ii) EMBOSS 2.6.0 is out. (iii) The first EMBOSS programming course will be run on Thu/Fri next week. (iv) NULLOK has been added to seqin.

Thomas reported that a bug in prettyplot ACD file had been identified but not fixed yet.

Bijay mentioned he'd written a parser and layout script for a Lion customer.

Claude reported that the EMBOSS Corba server is almost finished in its basic form. There is no encryption of client requests and it wont be possible to add that for a few months yet for technical reasons. He is looking at the GLOBUS grid library toolkit for Java for setting up web interfaces.

Shamilla is working on a Web Services wrapper for EMBOSS, uploading files and related issues.

Adam is rewriting b-tree indexing code in C++.

Peter is looking into (i) a replacement for the GCG peptidestructure/plotstructure programs. (ii) A replacement for the GCG RNA folding program. (iii) Writing wrappers for on-line applications such as BLAST. (iv) Database access methods such as ORACLE. (v) Reading PROSITE patterns. (vi) qa-testing for EMBASSY applications.
He is updating the code for reading feature tables. He is writing an application to replace the use of -acdpretty and -acd options. He will extend seqret for reading multiple feature tables.

Damian reported that the EMBnet education committee is looking sympathetically at his documentation project.

Jon (with Alan) is writing the EMBOSS programming course to be held next week.

Tim reported that (i) JEMBOSS/EMBOSS had been compiled / installed on an OSF m.c. in Denmark. (ii) Release 1.0 of JEMBOSS is available in EMBOSS 2.6. He has fixed several bugs (slow scrollbar, working directory not being saved between sessions etc) in JEMBOSS. He will be working on a multiple sequence alignment editor. He is writing (with Alan) a JEMBOSS paper for Bioinformatics.

Hugh reported that he has finished converting the graphical output of applications in X3D format. There are 5 jobs to do with grout before it becomes available (xml parsing, text display, output of meta data, multiple windows displaying separately, sequence display). He is thinking about a viewer in OpenGL.

Gary reported that sirna has been commited and that he is working on twofeat (which looks for features that are next to each other).

Lisa is in the middle of an overhaul of the documentation. The documentation standards were commented on and accepted in the altered format. They should now form the basic standard for any new program in EMBOSS.

2. A.O.B.

3. Date Of Next Meeting

Next meeting to be held at 9.30 on Feb 7, Loft Room 2