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Egon WillighagenBrowsing Internet Technologies
Exemplarchem 29 October 2004                     Browsing Internet TechnologiesWorld Wide Web ???
Exemplarchem 29 October 2004                                Browsing Internet TechnologiesWorld Wide Web ???• “The Web is ...
Exemplarchem 29 October 2004                            Browsing Internet TechnologiesOutline• Introduction to the WOC• Ar...
Exemplarchem 29 October 2004                                 Browsing Internet TechnologiesIntroduction to the WOC• Starte...
Exemplarchem 29 October 2004                                  Browsing Internet TechnologiesArchitecture of the WOC• XML b...
Exemplarchem 29 October 2004                                   Browsing Internet TechnologiesWeb Technologies in the WOC• ...
Exemplarchem 29 October 2004                                 Browsing Internet TechnologiesImages and Animation• Static Im...
Exemplarchem 29 October 2004                                Browsing Internet TechnologiesJmol• Applet with few requiremen...
Exemplarchem 29 October 2004                                  Browsing Internet TechnologiesJmol Scripting• Rasmol/Chime S...
Exemplarchem 29 October 2004                      Browsing Internet TechnologiesInternal and external Hyperlinks          ...
Exemplarchem 29 October 2004                                                             Browsing Internet Technologies   ...
Exemplarchem 29 October 2004                                 Browsing Internet TechnologiesExternal Hyperlinks: DADML•   h...
Exemplarchem 29 October 2004                                                         Browsing Internet Technologies       ...
Exemplarchem 29 October 2004                                 Browsing Internet Technologies Conclusion• New technologies a...
Exemplarchem 29 October 2004                               Browsing Internet Technologies Acknowledgments• Micha Fleuren a...
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Exemplarchem london 2004-10-29

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Transcript of "Exemplarchem london 2004-10-29"

  1. 1. Egon WillighagenBrowsing Internet Technologies
  2. 2. Exemplarchem 29 October 2004 Browsing Internet TechnologiesWorld Wide Web ???
  3. 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. 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. 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. 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. 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. 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. 9. Exemplarchem 29 October 2004 Browsing Internet TechnologiesJmol• Applet with few requirements – Displays molecules, proteins and crystals – Shows vibrations and animations
  10. 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. 11. Exemplarchem 29 October 2004 Browsing Internet TechnologiesInternal and external Hyperlinks Topic Map DADML
  12. 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. 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. 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. 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. 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/
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