Exemplarchem london 2004-10-29

Browsing Internet TechnologiesEgon Willighagen

World Wide Web ???

Browsing Internet TechnologiesExemplarchem 29 October 2004

World Wide Web ???

• “The Web is a distributed hypertext system that operates over the Internet. Hypertext is browsed using a program called a web browser which retrieves pieces of information from web servers and displays them on your screen.”

http://wikipedia.org/

• Fuzzy Definition !!!– UseNet, email?

– External programs? What's a browser anyway?

– HTTP protocol only?

– Port 80 only?


Outline

• Introduction to the WOC

• Architecture of the WOC

• Browsing Internet Technologies1. Topic Maps

2. DADML

3. CMLRSS

4. Jmol


Introduction to the WOC

• Started in 1996 as educational tool using university servers

• As project got bigger in size, aims became two fold– give an overview of high school and university level organic

chemistry

– explore and try applicable Internet technologies

• Dictionary instead of Presentation– applying world wide web paradigm

• many links, both internal and external

– applying early conclusions on Internet usage

• short texts, no overuse of colors

• Important: must run on all browsers


Architecture of the WOC

• XML based source– easily convertible to multiple formats (HTML, PDF)

– availability of free XML processing tools

– allows combining all kinds of information

• HTML Website– Frames for clear layout (outdated)

– Hyperlinking (menu, buttons etc)

– Integration with other resources on the Internet

– Browsers integrate

• plugins and applets

• external applications (e.g. chemical MIMEs)


Web Technologies in the WOC

• Interactivity with User– auto generated pages with cgi-bin

– moving molecules (Jmol)

– external applications using ChemicalMime

• Internal Hyperlinks– only autogenerated HTML links <a href=””>

– Topic Maps

• External Hyperlinks– Internet search

– Links with other database (DADML)

• Keep them coming back...– easy/fun to use and quality

– user binding (CMLRSS)


Images and Animation

• Static Images– Static using GIF, PNG etc

• Animations– animated GIF

– later came Flash and SVG

• Molecular species– Jmol


Jmol

• Applet with few requirements– Displays molecules, proteins

and crystals

– Shows vibrations and animations


Jmol Scripting

• Rasmol/Chime Scripting– color each atom separately

• high lighting specifics

– control display features separately

• protein: overall cartoons but active site space filled

• JavaScript interaction with applet from HTML– library (Jmol.js)


Internal and external Hyperlinks


Topic Map

DADML

Internal Hyperlinks: Topic Maps<topicmap xmlns="http://www.topic-maps.de/content/resources\tm.dtd">

<assoc id="at-is-de-homoloog-met-een-koolstof-meer-van">

<assocrl xlink:href="methaanzuur"/></assoc>

<assoc id="at-is-de-homoloog-met-een-koolstof-minder-van">

<assocrl xlink:href="propionzuur"/></assoc>

<assoc id="at-heeft-als-zuurrest">

<assocrl xlink:href="acetaat"/></assoc>

<assoc id="at-is-een-der">

<assocrl xlink:href="alkaanzuren"/></assoc>

<assoc id="at-is-een-der">

<assocrl xlink:href="oplosmiddelen"/></assoc>

</topicmap>


External Hyperlinks: DADML

• DADML: Database Access Definition Markup Language

defines how URLs can be composed using only an index and index type

dadml://any/cas-number?64-19-7


• http://webbk.nist.gov/cgi/cbook.cgi?ID=64-19-7&Units=SI&Mask=80

Rich Site Summary

• News feed to keep users informed about changes on website– one feed about website

– one CMLRSS feed about database changes


P. Murray-Rust, H.S. Rzepa, M.J. Williamson, and E.L. Willighagen, J.Chem.Inf.Comp.Sci., 2004, 44(2):462 - 469

Conclusion

• New technologies are being developed– Non-static molecular information (Jmol)

– but chemists need to apply those to chemistry themselves

• Use most advanced technologies, but keep in mind:– to focus on the information, not the format

– the basics of web page design

• light design

• few links to wanted information

• WOC has been excellent platform for testing new technologies


Acknowledgments

• Micha Fleuren and Geert Josten (WOC)

• Dan Gezelter (Notre Dame University) and Miguel Howard (Jmol)

• Jmol: http://www.jmol.org/


Technology

Exemplarchem london 2004-10-29