Figure 2

Example scripts for Bioclipse 2. The Bioclipse Scripting Language in Bioclipse 2 is based on Javascript with extensions contributed by plugins. Here are two example scripts that demonstrate several integrated components: a) PubChem is queried for compounds matching the name "HIV" using a Web service, substructures are isolated that contain pyrrolidine and opened for inspection, Balloon is used to generate 5 3D conformations of the first match, and finally the conformations are saved to an SDFile. b) Two nucleotide sequences are downloaded from EMBL using the WSDbfetch Web service at EBI, translated to protein using Biojava, and aligned using the Kalign Web service at EBI. The complete examples are available as gists from github with id: a) 163575 and b) 163440.