Subject: Java and other WWW developments

From: "Paul Weber" <[email-masked]>
Date: Tue, 9 Apr 1996 09:31:34 -0500

Hi,

First, I'm glad that Steve Bachrach and others have been impressed with the
recent web developments for chemistry, including the Java-based "Sketch
and Fetch" tool we created here.   From my research, it is clear that
chemistry users are among the growing population of computer users who are
finding that Browsers and Java make distributed computing a heck of a
lot easier than copying files over ftp.   Silicon Graphic's recent
announcement of Molecular Inventor (now in beta) is another indicator of
how computational chemistry is about to change very much, and very quickly.
(And you can use Molecular Inventor with SYBYL as well -- Steve only
mentioned SGI and MSI and hey, I hate being overlooked!).  For more
information about Molecular Inventor, see the SGI homepage (check under
"News") at www.sgi.com.   I'm also surprised to see the attention focused
just on Java -- if all you want to do is look at a molecule, you might
consider VRML as well as Molecular Inventor for getting a much improved
display quality.  VRML and MI formats are pretty easy to write too, so
general support in the future seems to be a good bet.

Now about Java -

The download times are a drawback that many have noted, and many are
working on.  Downloading the classes once and storing locally is
probably the best bet, as long as the application remembers to check
to see if it is still up to date.

I don't think anyone should lose sleep or waste time worrying about the
multitude of Java Applets that could be coming available.   Having many
Java applets out there is NOT the issue.

First, writing an applet to rotate a molecule is **pretty darn easy** (see
the example in the Sun Java release).  But more important, I see Java and
Web technology as the ultimate integrator -- you will be able to construct
web pages for your work, where you could mix and match applets from different
vendors.  Thus, a "plug and play" of applications.   The real issue then
is will there be a common data format to drag and drop between applets?
Again, I think the Molecular Inventor format from SGI comes the closest
to what we could use (and Tripos is using it, as well as MSI and probably
other vendors, too).

A common vision is to think of the Browser as the new desktop, or GUI to
your work.   You might, in the not too distant future, get a chemistry
version of "plug and play" where a molecule sketched in a Tripos applet is
used to pull out compounds from an MDL database, some of which are then
minimized using the Merck FF, all on the same page (which could then be
stored or "registered" as a notebook page that could be searched later).

I think that it is a good time for the community to search for acceptable
standards, such as SGI's Molecular Inventor, Tripos's SLN, DayLight's
SMILES, or the PDB (yuck). The chemistry community could then promote the
use of these standard formats by all software producers, whether garage-shop,
grad student, or public company.

Watch the Web for more big developments soon!

-- 

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Paul L. Weber, Ph. D.
Vice President, Product Development      Phone: 314 647 1099
Tripos, Inc.                               Fax: 314 647 9241
1699 S. Hanley Rd 
St. Louis MO 63144 USA               Email: [email-masked]
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