Exemplarchem london 2004-10-29
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Transcript of 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?
Browsing Internet TechnologiesExemplarchem 29 October 2004
Outline
• Introduction to the WOC
• Architecture of the WOC
• Browsing Internet Technologies1. Topic Maps
2. DADML
3. CMLRSS
4. Jmol
Browsing Internet TechnologiesExemplarchem 29 October 2004
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
Browsing Internet TechnologiesExemplarchem 29 October 2004
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• HTML Website– Frames for clear layout (outdated)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)
Browsing Internet TechnologiesExemplarchem 29 October 2004
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)
Browsing Internet TechnologiesExemplarchem 29 October 2004
Images and Animation
• Static Images– Static using GIF, PNG etc
• Animations– animated GIF
– later came Flash and SVG
• Molecular species– Jmol
Browsing Internet TechnologiesExemplarchem 29 October 2004
Jmol
• Applet with few requirements– Displays molecules, proteins
and crystals
– Shows vibrations and animations
Browsing Internet TechnologiesExemplarchem 29 October 2004
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)
Browsing Internet TechnologiesExemplarchem 29 October 2004
Internal and external Hyperlinks
Browsing Internet TechnologiesExemplarchem 29 October 2004
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>
Browsing Internet TechnologiesExemplarchem 29 October 2004
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
Browsing Internet TechnologiesExemplarchem 29 October 2004
• 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
Browsing Internet TechnologiesExemplarchem 29 October 2004
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
Browsing Internet TechnologiesExemplarchem 29 October 2004
Acknowledgments
• Micha Fleuren and Geert Josten (WOC)
• Dan Gezelter (Notre Dame University) and Miguel Howard (Jmol)
• Jmol: http://www.jmol.org/
Browsing Internet TechnologiesExemplarchem 29 October 2004