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Exemplarchem london 2004-10-29

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  • 1. Egon WillighagenBrowsing Internet Technologies
  • 2. Exemplarchem 29 October 2004 Browsing Internet TechnologiesWorld Wide Web ???
  • 3. Exemplarchem 29 October 2004 Browsing Internet TechnologiesWorld 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? Whats a browser anyway? – HTTP protocol only? – Port 80 only?
  • 4. Exemplarchem 29 October 2004 Browsing Internet TechnologiesOutline• Introduction to the WOC• Architecture of the WOC• Browsing Internet Technologies 1. Topic Maps 2. DADML 3. CMLRSS 4. Jmol
  • 5. Exemplarchem 29 October 2004 Browsing Internet TechnologiesIntroduction 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
  • 6. Exemplarchem 29 October 2004 Browsing Internet TechnologiesArchitecture 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)
  • 7. Exemplarchem 29 October 2004 Browsing Internet TechnologiesWeb 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)
  • 8. Exemplarchem 29 October 2004 Browsing Internet TechnologiesImages and Animation• Static Images – Static using GIF, PNG etc• Animations – animated GIF – later came Flash and SVG• Molecular species – Jmol
  • 9. Exemplarchem 29 October 2004 Browsing Internet TechnologiesJmol• Applet with few requirements – Displays molecules, proteins and crystals – Shows vibrations and animations
  • 10. Exemplarchem 29 October 2004 Browsing Internet TechnologiesJmol 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)
  • 11. Exemplarchem 29 October 2004 Browsing Internet TechnologiesInternal and external Hyperlinks Topic Map DADML
  • 12. Exemplarchem 29 October 2004 Browsing Internet Technologies Internal Hyperlinks: Topic Maps<topicmap xmlns="http://www.topic-maps.de/content/resourcestm.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>
  • 13. Exemplarchem 29 October 2004 Browsing Internet TechnologiesExternal Hyperlinks: DADML• http://webbk.nist.gov/cgi/cbook.cgi?ID=64-19-7&Units=SI&Mask=80• DADML: Database Access Definition Markup Language defines how URLs can be composed using only an index and index typedadml://any/cas-number?64-19-7
  • 14. Exemplarchem 29 October 2004 Browsing Internet Technologies Rich Site Summary • News feed to keep users informed about changes on website – one feed about website – one CMLRSS feed about database changesP. Murray-Rust, H.S. Rzepa, M.J. Williamson, and E.L. Willighagen, J.Chem.Inf.Comp.Sci., 2004, 44(2):462 - 469
  • 15. Exemplarchem 29 October 2004 Browsing Internet Technologies 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
  • 16. Exemplarchem 29 October 2004 Browsing Internet Technologies Acknowledgments• Micha Fleuren and Geert Josten (WOC)• Dan Gezelter (Notre Dame University) and Miguel Howard (Jmol)• Jmol: http://www.jmol.org/