EMBOSS: Project Meeting (Fri 7th March 2003)


HGMP: Alan Bleasby, Gary Williams, Terry Stewart, Hugh Morgan, Damian Counsell, Jon Ison, Lisa Mullan
Cambridge Uni:
EBI: Peter Rice, Adam Lowe

Apologies: Bijay Jassal, Thomas Laurent and Dave Judge

1. Minutes of the last meeting

Minutes of the meeting of 21st February 2003 are here

2. Outstanding action points

From previous meetings:
More warnings for bad ACD files will be introduced (PMR, 2003-02-21)
Developers should report typical ACD mistakes to PMR (all, 2003-02-21)
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)
DAM has also requested training materials (action LJM, 2003-02-21)
Teaching materials for SM (action LJM, 2003-02-21)
Reasons why local people should start using EMBOSS for SM (action all, 2003-02-21)
Help with setting up a Jemboss client/server if appropriate for SM (action TJC, 2003-02-21)
CCP11 mentioned on EMBOSS pages (action AJB/GWW, 2003-02-21)

From this meeting:
Organise two meetings for (i) EMBOSS for MS Windows, (ii) coding standards (JCI)
Commit test data for domainatrix applications (JCI)
Investigate possibilities of Microsoft funding for developing EMBOSS for Windows (DC)
Look into binary downloads for MAC OS 10 (AL)
Research automatic conversion of html to docbook (Adam can provide a script to help with the reformatting) (TJS)
Prepare training course / demo on "Documentation of EMBOSS Software" (the use of XML Mind etc) (DC & TJS)
Advertise forthcoming EMBOSS Programming Course(s) (JCI)

3. Progress on action points

The following tasks have been completed:
APL requested a username on the development machines (AJB, 2003-02-21)
An example output format for new descriptions of the help tables will be circulated (GWW, 2003-02-21)
A list of programs unique to EMBOSS for SM (action GWW, 2003-02-21)

4. Software Development

4.1 Standardised error messages for emboss.defaults and ACD files (PMR)

4.2 Report extensions; removing the score, correcting sequence ranges (PMR)

4.3 What is the best route for establishing and implementing coding standards? (JCI)

It was decided that this would be discussed at a separate meeting (JCI to arrange).

Alan reported that the testcode application is complete.

5. Documentation

5.1 Is docbook the way to go for documentation? (LM)
There was general agreement that docbook is the way to go, provided there is appopriate training and support.

Alan / Lisa reported they have been documenting testcode. The idea is that the documentation will be a "gold standard" for other applications.

6. Windows versions of EMBOSS

Comments from DJ that were discussed at the meeting follow:
Please could you get them to discuss windows versions of emboss and web access to facilities that cannot practically be run on desktop machines.
Underlying message/opinion is that for a large proportion of potential EMBOSS users (the ones Lisa and I meet) it is more sane to run the applications on their desktop machines. jemboss is wonderful, but it is not (yet) a total solution for eveyone. A windows (macos X) version of EMBOSS plus a local GUI (possibly Staden's spin after substantial improvements .... or local version of jemboss ... or whatever) is the obvious solution for these chaps. Their alternative (here at least) is Vector NTI and similar ... !!!
I would be interested on possibilities of windows EMBOSS. I am anxious to set up a new "EMBOSS and Staden on your workstation" course ... just as soon as next version of Staden is out, as current version not quite up to it.
Also, maybe the provision of a web interface for all EMBOSS applications that will not run sensibly on a machine without local sequence databases. I.e. anything that is any sort of database search (e.g. fuzznuc and friends). I suggest an important part of the future of EMBOSS is as a package (with suitable frontend ... Staden, local version of Jemboss, whatever ...) which runs on desktop PCs and accesses sequence databases remotely via SRS.

It was decided that a windows versions of EMBOSS would be discussed at a separate meeting (JCI to arrange). We all agreed it's a good idea to approach Microsoft for funding the development of EMBOSS for Windows; Damian will look into the possibilities.

7. AOB

Hugh will demonstrate grout at a training course in early April, but grout will not be used in the training exercises themselves.
Adam suggested that the XML files that grout uses are compressed before being passed over the net.
Jon reported that he is rewriting completely the protein structure library code (ajxyz.c/h) and that suggestions are welcome.
Alan reported that the first EMBOSS programming course ("Bioinformatics Software Development Course") went well, and that three more are booked. Jon is to advertise them soon.
Alan reported that --with, --docroot and --withgccprofile have been added.
Gary reports that:
Showseq and showfeat both now have the qualifier '-stricttags'. By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If '-stricttags' is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed.
Megamerger now has the qualifier '-prefer' which makes it use the first sequence to create the merged sequence whenever there is a mismatch between the two sequences.
Sirna now has the qualifier '-context' which writes the first two bases (in brackets) of the 23 base target region.
Maskseq and maskfeat now both have the qualifier '-tolower' which will change the masked regions to lower-case characters instead of replacing them with a mask character.

3. Date Of Next Meeting

Next meeting to be held at 9.30 on Mar 21, Loft Room 2