Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Mitch S. <mit...@be...>]

Hi Ann!  Congratulations on your professorship.

On Mon, 2007-04-30 at 13:11 -0500, Ann Loraine wrote:
> Did anybody mention Java Web Start as an alternative method of
> deploying java applications?

I've had a nice experience using Web Start applications before, and it
does solve some of the problems with applets.

I think the biggest objection to Java (that I haven't seen anyone
mention in this thread yet) is that it's been tried.  Given your list of
links, it looks like people have already implemented genome browsing
using Java Web Start, and still UCSC seems to be the browser everyone
uses.  

Admittedly, my direct experience with non-computational biologists is
mostly limited to human and mouse researchers, but talking with people
at the RECOMB poster session reinforced my sense that UCSC is the main
one.

So while the language question does deserve consideration, I think the
more important question is, why is UCSC so popular?  It can't be 100%
inertia.  The Java drawbacks that people have mentioned are all good
points, and I'd add that java app(let)s are often not entirely a part of
the web, in that it takes extra effort to make them bookmarkable and
linkable and to follow links from within them.  And the network effects
you get from being part of the web are pretty huge.  Which reminds me
that we need to do a better job of linking out and being bookmarkable
and linkable.

The Java Web Start approach seems even more non-web than applets.  Is it
even possible to have an html link that takes you to a specific region
in a Java Web Start-using genome browser?

The volume of data that UCSC makes available is also a pretty big
strength.

Also, maybe this is a cheap shot, but on the PlantIGB page I see this:
================
Click here if your computer has at least 1 gig of memory.
Click here if your computer has at least 786 meg of memory.
Click here if your computer has at least 512 meg of memory.
================
which is very much not the face I'd like to present to the
non-computer-savvy biologists out there.

Regards,
Mitch