EMBOSS: Project Meeting (Fri 25th July 2003)


HGMP: Gary Williams, Alan Bleasby, Tim Carver, Jon Ison, Claude Beazley, Hugh Morgan, Damian Counsell, Lisa Mullan,
Lion: Thomas Laurent
Cambridge Uni:
EBI: Peter Rice, Adam Lowe
Visitors: Karl Podester


Minutes of the last meeting

Minutes of the meeting of 11th July 2003 are here

1. Action points

1.1 From this meetings:
Look at converting Phylip documentation to EMBOSS (action GW, 2003-07025)

1.2 From previous meetings:
ACD docs need updating (action PMR, 2003-02-21)
MEME documentation is required (action AJB, 2003-02-21)
Provide documentation for propehcy (AJB, 2003-03-21)
Inform GES guys of licensing issues wrt wordmatching algorithm. (action PMR, 2003-07-11)

1.3 Progress on action points
Move CCP11 banner to top of EMBOSS homepage (action GW, 2003-07-11)
Research automatic conversion of html to docbook (Adam can provide a script to help with the reformatting) (TJS, 2003-03-07)
Look into binary downloads for MAC OS 10 (AL, 2003-03-07)

1.4 The following action points are postponed until further notice
Prepare training course / demo on "Documentation of EMBOSS Software" (the use of XML Mind etc) (DC & TJS, 2003-03-07)
Jon mentioned he won't have time to approach industry for funding.

2. Software Development

2.1 "The user perspective revisited" (AJB)
Alan mentioned that there are 4 routes to better inform the user of the best route to find appropriate EMBOSS programs: 1) Documentation and training, 2) Intelligent agent query of documentation taking a "task centred" view, 3) JEMBOSS, 4) Specialised GUI's / workflow etc.
Damian spoke about the proposed expert system, Peter mentioned Taverna as an option for workflow, Jon suggested an enhanced web page for potential contributors to encourage contributions, Claude suggested seeking industry support for EMBOSS development.

2.2 "Phylip integration" (PMR)
2.2.1 new ACD data types
Peter has been working on Phylip configuration, he's added 5 new ACD datatypes; 1) seqsetall (used like a USA), 2) phylogenetic trees, 3) distances matrices that handle square, upper and lower triangle phylip formats, 4) properties (weights, ancestral states and multistate factors), 5) frequency data and 6) discrete states. The Phylip interface looks much simplified with these ACD types added.
2.2.2 documentation
Peter mentioned that documentation is available for Phylip. Gary will look at adapting this for EMBOSS.

2.3 "Jemboss now has the code to cope with GROUT graphics!" (TC)
Timhas committed JEMBOSS code which is ready for grout when it arrives. Peter will make integrating grout and plplot a priority once phylip stuff is done.

2.4 "JAligner" (TC)
Tim reported that JAligner, which is a Smith-Waterman java interface (http://foobox.com/~ahmed/jaligner) might be incorporated into JEMBOSS or the alignment editor.

2.5 "JEmbosS Sequence Editor - JESSE" (TC)
Tim said that he was going to announce JESSE on the EMBNet node and ask for collaborators.

3. Documentation & Training

3.1 "State of play of EMBOSS books" (DC)
Damian gave a summary of the state-of-play. We'll reach a final decision at the next EMBOSS meeting.

4. Administration

5. AOB

Karl mentioned he'd give a code review at the next EMBOSS meeting.

6. Date Of Next Meeting

Next meeting to be held at 9.30 on August 8 2003, Pompeiian Room, Hinxton Hall