EMBOSS: Project Meeting (Fri 21st March 2003)


HGMP: Alan Bleasby, Gary Williams, Hugh Morgan, Damian Counsell, Jon Ison, Claude Beazley, Tim Carver
Cambridge Uni:
EBI: Adam Lowe

Apologies: Bijay Jassal, Thomas Laurent, Dave Judge, Peter Rice

1. Minutes of the last meeting

Minutes of the meeting of 7th March 2003 are here

2. Outstanding action points

From previous meetings:
EMBASSY QA tests need incorporating (PMR, 2003-02-21)
ACD log file too verbose & old ACDpretty to be removed (PMR, 2003-02-21)
ACD docs need updating (action PMR, 2003-02-21)
MEME documentation is required (action AJB, 2003-02-21)
Help with setting up a Jemboss client/server if appropriate for SM (action TJC, 2003-02-21)
Look into binary downloads for MAC OS 10 (AL, 2003-03-07)
Research automatic conversion of html to docbook (Adam can provide a script to help with the reformatting) (TJS, 2003-03-07)
Prepare training course / demo on "Documentation of EMBOSS Software" (the use of XML Mind etc) (DC & TJS, 2003-03-07)

From this meeting:
Provide GW with text thanking providers of emboss machines for their support (AJB, 2003-03-21)
Provide documentation for propehcy (AJB, 2003-03-21)
Approach Michael Herbert about RedHat Linux distribution for bioinformatics. (DC, 2003-03-21)
Preliminary look into DTI funding for EMBOSS (DC, 2003-03-21)
Preliminary look into industry funding for EMBOSS (JCI, 2003-03-21)

3. Progress on action points

The following tasks have been completed:
Developers should report typical ACD mistakes to PMR (all, 2003-02-21)
More warnings for bad ACD files will be introduced (PMR, 2003-02-21)
DAM has also requested training materials (LJM, 2003-02-21)
Teaching materials for SM (LJM, 2003-02-21)
Reasons why local people should start using EMBOSS for SM (all, 2003-02-21)
CCP11 mentioned on EMBOSS pages (AJB/GWW, 2003-02-21)
Organise two meetings for (i) EMBOSS for MS Windows, (ii) coding standards (JCI, 2003-03-07)
Commit test data for domainatrix applications (JCI, 2003-03-07)
Investigate possibilities of Microsoft funding for developing EMBOSS for Windows (DC, 2003-03-07)
Advertise forthcoming EMBOSS Programming Course(s) (JCI, 2003-03-07)

4. Software Development

4.1 Integration of protein structure with EMBOSS. (i) Quick update. (ii) Requests / requirements ? (JCI)
Jon reported that he has written a hierarchy of data structures for holding data from a PDB file. He asked everyone to think about EMBOSS requirements for protein structure and to send him any suggestions.

Tim reported that he might be commiting his alignment editor fairly soon.

5. Documentation

Gary reported that he'd revamped the history page and that tcode "gold standard" documentation was complete.

6. Administration

Alan reported that he'd been working on configuration.

6. Update on EMBOSS for M$ Windows proposal (DC)

Damian reported that that he'd had discussions with the head of MS Research and that he, PMR, RL, AJB and JCI had met to discuss a MS version of windows. In summary: (i) Full GUI version of EMBOSS is desirable, (ii) funding for 2 people either based at home or MS Research, (iii) support is as important as development and should be worked into the approach, (iv) release of linux version should not be delayed by MS version, (v) version should be EASY to install, one-click installation ideally, (vi) Peter will give a presentation to MS.

7. AOB

PMR is looking into automating the updating of ACD docs, and will remove the old ACDpretty and make the ACD log file less verbose after the next release.

3. Date Of Next Meeting

Next meeting to be held at 9.30 on Apr 4, Loft Room 2