EMBOSS: Project Meeting (Fri 21st February 2003)


HGMP: Alan Bleasby, Hugh Morgan, Tim Carver, Gary Williams
Cambridge Uni: Sylvia Martinelli
EBI: 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)

4. Documentation

TJC/AJB have submitted a paper on the software design of Jemboss to Bioinformatics. 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).

5. Administration

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 (action TJC)

6. CCP11

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.

7. AOB

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