pointers to WWW6 D-Day XML track demos?

Peter Murray-Rust Peter at ursus.demon.co.uk
Wed Apr 16 08:53:41 BST 1997

In message <199704160553.WAA06008 at boethius.eng.sun.com> bosak at atlantic-83.Eng.Sun.COM (Jon Bosak) writes:
> [Mike_Spreitzer.PARC at xerox.com:]
> | I attended the XML track of WWW6 D-Day, and found it interesting.  I'd
> | like a list of links to the demos and/or information about what was
> | demoed.  When I asked Jon Bosak for this, he said it hadn't been

A semi-virtual demonstration of my browser JUMBO was given by Jon Bosak.  I
have written a README for this which is appended below.  This represents a 
'snapshot' of JUMBO (and CML) development at D-Day which will be preserved
as a (hopefully) working demonstration.  Several people have offered to set
up XML sites and have indicated that they will mirror this snapshot.
*** AS stressed below, I shall continue to develop JUMBO to track the drafts, 
but the snapshot will not be updated.***

Current links are:

and, hopefully, in emerging mirror XML sites.

I am extremely grateful to Jon for demo'ing this.  I've never met Jon - we had
a phone call about the demo - and I think it is tremendous what he achieved,
especially with all the rest that was happening.  My limited feedback was that
it went well (Jon mentioned that it is slow, and that's because it is Java, and
large (about 500 Kbytes of *.class).   Much of the size is due to the 
applications.  My own experience is that there can be a factor of ~10 between 
apparently equivalent platforms.).  So congratulations, Jon!
One of the many positive messages is that this representa a *self-contained*
XML system independent of the networks.  {OK, this isn't the main rationale
for XML, but it comes as a free bonus!}  So the package can be put on CDROM
and run by people who have never heard of XML or Java and who aren't allowed
on the WWW (yes, they exist).  The HTML_browser/XML/Java combination is
therefore exactly what many technical publishers may want for run-anywhere,
installation-free manuals, reports, etc.

Some conventional dead-trees describing the demo were shipped but failed to
make it.  The main content of these is in:
within the distribution.
	There are also copies of the demo under:
Since I wanted people to be able to see at the back, the font has been ramped
up in some of the *.html files and you may want to edit these for some 
platforms.  [JUMBO also has its own font selection mechanism both through
'menus' and PIs in the documents, which you may wish to edit.]
    ***************************   README  *******************************

			JUMBO and XML/CML demonstration

This package is a snapshot at April 11 1997 of the development of:

	- Chemical Markup Language (an application of XML)
	- JUMBO (a Java-based browser for XML documents)
	- Java *.class add-ons for molecular processing
	- examples of the Virtual Hyperglossary project in XML
	- example files, data, glossaries, etc.

and is arranged as a self-explanatory demonstration.

The material was demo'ed at WWW6 1997 at Santa Clara by Jon Bosak of SUN
Microsystems.  Many thanks, Jon!

The distribution contains (at least):
	demos			the top directory
		pmr		the JUMBO classes and the molecular software
		PLAY		classes to display Jon's Shakespeare XML
		glossary 	a range of glossaries
		swissdata	a small number of SWISSPROT files in XML
		icons 		some icons for Jumbo and classes
		*.cml, *.xml	Example CML and/or XML files
		*.mol, etc.	Files in chemical/* MIME
		*.html		files to drive applets, demos, etc.
		w3_*.html	the W3 demo (start with w3_index.html)
		index.html	start of a more advanced demo

The subdirectories contain:
		12620		terms from ISO12620 for terminology
		cif		Crystallographic Information File
		jcamp		terms from JCAMP spectroscopic standard
		local		miscellaneous terms
		mol		BUILTIN terms for CML
		pdb		embryonic - terms from Protein Data Bank manual
		swissprot	terms from Swissprot manual
		tecml		BUILTIN terms from TecML
		units		SI units

(NOTE:  The contents of the glossary entries are copyright the original 
authors.We have collaborated with all of these and are extremely grateful for 
permission to produce edited glossaries under XML.  No material has been
deliberately edited (other than for software compatibility and formatting).

		euclid, util	utility classes
		simplegraph	customisation of Java AWT
		molecule	support for molecular properties
		sgml		application-independent XML support
		stat		simple statistics
		cml		CML support routines
		chemime		support for chemical/* MIME filetypes
To run the demo:

This distribution may be read by at least the following distinct groups:

	- those interested in XML
	- those interested in CML
	- those interested in the VHG

so parts of it may not be relevant to everyone.

The demo is arranged as an INSTALLATION-FREE distribution, after unpacking. You
need only a:

	Java-enabled browser (e.g. Netscape or Microsoft IE).

(if you aren't sure, check under the 'Options' on the menu and see if it has
'Java Console'.  If not, it's probably not Java-enabled (e.g. under Windows3.1))
If you have problems later, messages appear in the java console.

Simply load your browser and load the file 


This will give a brief overview of JUMBO and then give a series of demos which
should be automatic.  Points to note:

- it takes a little while to load the classes initially (perhaps 15-60 sec) but
subsequent *.html pages should be rapid.

- the windows need manually resizing.  (I have spent a LOT of time trying to
solve this problem and am now waiting for the next JDK).  Sometimes the windows
get hidden, and sometimes they don't come back after they have been closed.

- very occasionally the demo crashes.  In this case, restart the browser and
**clear the cache**.

- some windows, etc. take a few seconds to respond - be patient and don't click
the mouse more than once - you might get 10 windows!

This demo will teach you how to run JUMBO and you should become familiar with
the use of the folder icons in the tree, clicking on icons, etc.  If you then 
want to go onto a more molecular demo, go to:


[You shouldn't have to alter any setup on your machine.  However, occasionally
browsers do NOT need CLASSPATH set, and it may be worth removing this.]

Running JUMBO with other files.

JUMBO can be run BOTH as an applet (above) and as an application.  Another
way of running as an applet is 

	appletviewer foo.html

(This may be useful if foo.html crashes under a browser).

To run as an application you will need a Java interpreter (e.g. in JDK).  Then

	java pmr.sgml.SGMLTree <yourfile.ext> [<mymimetype>]

JUMBO will read XML files, ESIS files and chemical/* files.  [There may be
some restrictions (e.g. not all XML options are supported, although JUMBO
can interoperate with NXP or Lark - not in this distribution, I think).  Also
some chemical/* converters do not cover all the file (especially Gaussian,
MOPAC, etc.)].  JUMBO will use the MIMEtype if given, or else try to
deduce it from the extension (see mimtypes file).

	java pmr.sgml.SGMLTree 1ins.pdb
	java pmr.sgml.SGMLTree scene1.sgm text/xml
	java pmr.sgml.SGMLTree junk.foo chemical/x-mdl-molfile
	java pmr.sgml.SGMLTree bar.esis    
(I'm not sure whether the last works in this distribution)

JUMBO will read the DOCTYPE and try to load a DTD from dtd.classes.  If it 
fails it assumes a DTD of ANY.  It will then probably throw a large number of 
warnings that it can't identify GIs, but will still produce a display.

If you want to hack your own WF *.xml, feel free.  JUMBO tries to check for
content and may throw some warnings - ignore them.  JUMBO supports most of
XML up to March 31 1997, but some has no obvious rendering (e.g. ID->IDREF
has no icons or actions).  JUMBO guesses the element  title from Content, 
TITLE attribute or GI in that order.

Future Developments

XML is developing extremely quickly and the spec warns that you cannot rely on
anything within it to be 'final'.  Future developments in XML *will* be 
incompatible with this distribution :-).  CML is also developing and, again,
this is a snapshot of CML1.0.  CML1.0 is not completely XML-compatible - there
is no support for XML-LINK in the DTD, for example and the use of links
(XVAR | TYPE="URL") will be changed to accommodate XML.  I believe the XML
files are syntactically correct, but may not remain so.  So you are advised
to use only the components in this distribution, because they are unlikely
to interoperate with future ones.


There is a lot more CML and JUMBO stuff (including FAQs, tutorials, etc) at:
The VHG home page (including other glossaries, a mailing list, ideas of 
concept maps, etc.) is at:
The OMF is at:

and my home page is at:

Please mail me with ideas at:
peter.murray-rust at nottingham.ac.uk


Most of the material in this distribution is Copyright Peter Murray-Rust, 1997.
(The known exceptions are most of the glossaries, and Jon Bosak's Shakespeare).
My material is available for personal use and evaluation, but not for 
redistribution or use within packages whether academic or commercial (unless
agreement is obtained).  (It is my intention that JUMBO classes will be made
availble for widespread free distribution but will not be in the public 
Source code will not be available except to committed developers (e.g.
through the OMF).  However, JUMBO is structured so that it should be possible
to do what you want by either extending or overrriding JUMBO classes.  Since
JUMBO uses the TEI extended pointer search, it's possible to retrieve any 
subobject from any other.  A (slightly out-of-date) API is available on the
CML WWW tree above.

The author disclaims any responsibility for any loss or damage however caused 
and makes no representation of the suitability of this material for any purpose.



April 14 1997

Peter Murray-Rust, domestic net connection
Virtual School of Molecular Sciences

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