Luke McCarthy lukem at bioinfo.pbi.nrc.ca
Mon Jul 30 04:09:24 UTC 2001

Hi everybody,

On and off over the past year or so, I've been developing a GUI for the 
EMBOSS tools designed to operate over the web.  It's been listed at the 
EMBOSS web site for most of that time, but in the last month I've 
significantly improved it to the point where I think it could be very 
useful to the entire EMBOSS user community.  But I'd like a little help to 
that end.

Before I release this interface out into the wild, I'd like it to be as 
polished as possible.  I don't have a lot of time right now to do extensive 
testing of any kind ('testing' to this date has only involved one trial run 
of each application), plus I don't actually use many of these tools in 
practice, so I don't know if they're actually useful the way they're 
currently presented.  So I'd like to solicit your assistance as EMBOSS users:

If you could find the time to drop by 
http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html , try out your favourite 
EMBOSS tool, offer any suggestion or criticism that comes to mind, and 
definitely let me know if something doesn't work, I would be very 
grateful.  Criticism of the look and feel (colours, font size, general 
appearance) is appreciated, but all of that is eminently configurable 
through the use of style sheets (which means if you're using an older 
browser, this probably won't work very well for you), so it's not really 
too helpful.  What I'm really looking for are places where the interface is 
awkward or difficult to understand.  And support for the frame/page 
groupings that EMBOSS 2.0.0 allows will be coming in the next couple of 
days, before anyone suggests that.

About the interface itself: the scripts build the input collection pages on 
the fly, reading relevant information from the ACD files (incidentally, in 
the process of building this interface I've written an ACD->XML converter 
if anyone would find that useful ;)  Because of this, it's remarkably 
robust to changes in the tools themselves.  Even the menu is generated 
dynamically, so only those tools which are available on your system will be 
listed (for example, if you haven't installed the EMBASSY stuff it won't 
show up...)  You can also have the script dump all of the input collection 
pages and the menus to static HTML files if you're expecting heavy traffic 
and don't want to waste system resources...

Anyway, that's my story.  I strongly urge anyone who thinks a GUI for the 
EMBOSS tools would be a useful thing to drop by and help me make this one 
all that it can be.  Any questions can be directed to me personally if you 
don't want to clutter up the list.


Luke McCarthy
Bioinformatics Group,
Plant Biotechnology Institute,
National Research Council of Canada
lukem at bioinfo.pbi.nrc.ca

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