EMBOSS: Project Meeting (Fri 21st February 2003)
Alan Bleasby, Hugh Morgan, Tim Carver, Gary Williams
Peter Rice, Adam Lowe
1. Minutes of the last meeting
These were not available (holiday)
2. Matters arising
There were no matters arising
3. Software Development
PMR reported that emboss.default and ACD parsing had been
cleaned up. Two new environment variables were now available
emboss.default has been extended to allow "resources" for the
description of associated databases (e.g. REBASE) and to
facilitate writing, for example, BLAST wrappers.
AJB suggested that developer output should be under the control
of a development switch.
More warnings for bad ACD files will be introduced (action PMR).
Developers should report typical ACD mistakes to PMR (action all).
APL requested a username on the development machines (action AJB)
TJC reported that code had been committed for running Jemboss
jobs under GNQS and OpenPBS.
HM reported that most applications had been modified to produce
XML output that can be displayed by GROUT
AJB reported that work is underway trying to configure GLIB, GETTEXT,
Orbit-mt (etc) for the corba software. GLIB will also be required
for the current GROUT.
EMBASSY QA tests need incorporating (action PMR)
ACD log file too verbose & old ACDpretty to be removed (action PMR)
TJC/AJB have submitted a paper on the software design of Jemboss
O'Reilly are sending copies of the new Sequence Analysis In A
Nutshell book to AJB/LJM.
ACD docs need updating (action PMR)
MEME documentation is required (action AJB)
An example output format for new descriptions of the help
tables will be circulated (action GWW).
DAM has also requested training materials (action LJM).
SM reported her experiences of setting up EMBOSS at Cambridge
University. She requested:
A list of programs unique to EMBOSS (action GWW)
Teaching materials (action LJM)
Reasons why local people should start using EMBOSS (action all).
Help with setting up a Jemboss client/server if appropriate
AJB informed the group that it had been noticed that CCP11 was
not mentioned on the EMBOSS pages. As CCP11 fund two posts
a suitable form of wording will be produced (action AJB/GWW).
It may also be possible to combine the CCP11 programmers meetings
with the fortnightly EMBOSS meetings (when required) as most
people are common to both groups.
Tim reported by email that (i) work is being carried out on a sequence editor/analyser, (ii) he has talked with Tom Oinn about possible collaboration on an interface for their workflow model and (iii) he has fixed Jemboss results display problem which was found only on MacOSX.
3. Date Of Next Meeting
Next meeting to be held at 9.30 on Mar 7, Loft Room 2