Monday, 7 January 2008

Enhancing the web for scientists

Egon Willighagen, myself, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck and David Wild have just published a paper describing userscripts we have written to enhace and extend web sites for scientists:
Userscripts for the Life Sciences BMC Bioinformatics 2007,8, 487. (Open Access)

Userscripts are Javascript programs that are triggered to run in your web browser when you go to certain web pages. They can alter the content of the web page on-the-fly. For example, one of the userscripts described in the paper looks up all PDB IDs on a web page and adds a link to a webpage showing the structure. For userscripts to work, your browser (e.g. Firefox) needs a special extension (e.g. Greasemonkey).

Our userscripts are divided into two broad categories:
  • Interacting with the scientific literature
    • OSCAR3 running on HTML
    • Add quotes from Chemical blogspace and Postgenomic to DOIs
    • Add to Connotea
  • Linking to chemical and biological data sources
    • Enhancement of PubChem with 3D structures
    • PDB-Jmol userscript
    • Sechemtic
    • Add quotes from Chemical blogspace to molecules
All of these userscripts are available from the Blue Obelisk web site. For other relevant userscripts, search (the official repository for all userscripts) for userscripts with the tags "Chemistry" or "Biology".

Image credit: Spiders web by Lida Rose (CC BY-ND 2.0)

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