BioInformatics

• JSmol visualization

  

  The JSmol library is used widely for molecular structure visualization. It has envolved from a java and applet implemenation to a pure javascript implemetation features both webgl and html5 svg graphing techniques. Now the two implementation co-exist, with javascript verion more widely used for molecule less than 20000, and Java version used for large scale structure with higher performance.

  See example JSmol viewer at RCSB website

  This project is built upon the simplest jsmol example. It’s used to demonstrate protein structure with different configrations, using functions provided by JSmol javascript. The protein data is retrieved from the RCSB PDB protein data bank

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• Get DNA Sequence from web service and embeded genome browser

  

  Genome data resource are scattered in various data hubs, usually these data hubs provide apis for users to download data for their reseach. Also, genome browsers provide a visual cue for users to choose the data of interests.

  This demo implemented a couple of different data retrieval mechanism using apis provided by data hosting sites.

  Also, I demo a simple html widget overlay on top of the BioDalliance genome browser, which let user visually select a data range. The widget functionality is implemented using D3.brush

  Read More:

  • Add a data source to BioDalliance server
  • ICM Web GB Work Status Report Apr 8 2015