EMBOSS: Project Meeting (Fri 5th September 2003)

Attendees

HGMP: Alan Bleasby, Jon Ison, Hugh Morgan, Gary Williams, Miriam Portela
Lion:
Sanger:
Cambridge Uni:
EBI:
Visitors:

Apologies:

Minutes of the last meeting

Minutes of the meeting of 8th August 2003 are here

1. Action points

1.1 From this meetings:

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)
Look at converting Phylip documentation to EMBOSS (action GW, 2003-07025)

2. Software Development

2.1 Code tidy up (AJB)
Alan reported that a complete tidy up of the code is now finished. He will forward an updated version of the coding standards to Gary for inclusion on the web. It is most important developers adhere to these guidelines.

2.2 Database indexing (AJB)
Alan reported that the new indexing software has been finished, debugged and tested. ajseqdb.c/h and indexing programs are to be updated accordingly. The priority is, however, getting ACD adapted for Hughs graphics stuff.

2.3 32 or 64 bit (AJB)
Alan reported that indexing will work with 32 or 64 bit and it was generally agreed that 64 bit would be a good default.


Hugh reported that Grout works via java web start, running with Tims machine as a server. If you want to see, use the url http://u.hgmp.mrc.ac.uk:8080/GROUT/ (only programs that work are plotorf, dotmatcher, dottup, iep and sometimes pepinfo).
Java web start is a program that handles downloading the .jar files and handles the security and that, so the users just click on a link and get the program.

Gary reported
1)that Tim fixed a bug found with the 'setcase' flag in the consensus library, which is used to define the case at a position based on the score.
2)that an option to test that all sequences in a file are the same type has been requested for infoseq.
3)minor bug in infoalign fixed.

3. Documentation & Training

Gary will push forward the administration of the new documentation post.
Alan reported that Damian has produced a first draft outline of the programming book.

4. Administration

5. AOB

Jon reported that he is preparing a paper with Mat Blades that mentions EMBOSS heavily.
Alan reported that the paper he did with Tim on JEMBOSS should be coming out shortly.

6. Date Of Next Meeting

Next meeting to be held at 9.30 on September 19 2003, Pompeiian Room, Hinxton Hall