EMBOSS: Project Meeting (Fri 11th 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, Rodrigo Lopez
Visitors: Karl


Minutes of the last meeting

Minutes of the meeting of 27th June 2003 are here

1. Action points

1.1 From this meetings:
Move CCP11 banner to top of EMBOSS homepage (action GW, 2003-07-11)
Inform GES guys of licensing issues wrt wordmatching algorithm. (action PMR, 2003-07-11)

1.2 From previous meetings:
ACD docs need updating (action PMR, 2003-02-21)
MEME documentation is required (action AJB, 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)
Provide documentation for propehcy (AJB, 2003-03-21)

1.3 Progress on action points
Approach Malcolm Herbert about RedHat Linux distribution for bioinformatics. (DC, 2003-03-21)

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)
Preliminary look into industry funding for EMBOSS (JCI, 2003-03-21)

2. Software Development

2.1 PHYLIP 3.6 integration (PMR)
Peter reported on the conversion of Phylip 3.6 to EMBOSS. Treefile input and output will be added. Multiple tree formats might be added but there is not an immediate need for them yet. treedist is not added yet and it is very complicated and so will be split into component programs with related names.

2.2 New output formats to replace (most of) the remaining text outfiles (PMR)
Peter has looked at all programs that generate outfiles. The use of name-value pairs and tables would cover all of the cases. These would complement the use of reports and alignment outputs. He is drawing up plans for name-value pairs and tables and will consider options for generation of XML output.

2.3 XML output and input (PMR)
See above

2.4 Grout (PMR)
Peter has been tied up with Phylip and has not made huge progress on this yet. After discussions with Alan, Grout will be made (from a superficial perspective) to fit the plplot model to begin with although internally things will be done the Grout way. Code additions will be made to support both Grout and plplot.

Lisa reported that the pepinfo graphical output needs a second look at because it is confusing.

Gary mentioned that ajRandomSeed should be modified so as not to use the seconds from the clock for its seed (following from a user email message to the same effect).

There was an inconclusive "discussion" about whether coil prediction programs should be combined or kept separate.

3. Documentation & Training

3.1 EMBOSS book update (DC)
Damian reported that CUP are very interested in the EMBOSS books and have offered favourable terms. He will compile a list of the pro's and con's of the different publishers and email all concerned parties.

4. Administration

5. AOB

5.1 Test PC for Jemboss and Grout? (HM)
Hugh mentioned the requirement for a PC, possibly with removable disks, for checking the portability of his graphics stuff on different platforms (mostly M$). He and Alan will look into it.

5.2 CCP11 banner on EMBOSS homepage (AJB)
Alan reported that David Moss had requested the CCP11 banner was given at the top of the EMBOSS pages. There was general agreement this is a good thing.

5.3 GES wordmatching algorithm (PMR)
Peter reported that GES want to have their wordmatching algorithm included in EMBOSS. Peter will get in touch informing them of licensing issues.

5.4 Proposal for user-survery (JCI)
Jon suggested a user survey to assess user requirements related to e.g. lots of individual programs or fewer programs that combine related functionality. He suggested this might clarify the true requirements and avoid long and inconclusive discussions in EMBOSS meetings. There was no time left to discuss the idea.

6. Date Of Next Meeting

Next meeting to be held at 9.30 on July 25 2003, Loft Room 2