Depth-First: Tag visualization

Casual Saturdays: Balkanization

Rich Apodaca — Sat, 13 Sep 2008 17:04:00 +0000

3D Molecular Visualization on the Web: OpenAstexViewer

Rich Apodaca — Thu, 19 Jun 2008 09:04:00 +0000

OpenAstexViewer is an LGPL-licensed 3D molecular visualization tool written in Java. With the obfuscated jarfile weighing in at 1 MB, OpenAstexViewer could make a good choice for use in Web applications.

There are now at least two open source, feature-rich 3D molecular visualization tools written in Java (the other being Jmol). Are there any others?

Credit: thanks to Noel O'Boyle for spotting this.

Visualizing Cheminformatics Algorithms

Rich Apodaca — Fri, 17 Nov 2006 15:55:00 +0000

The Sorting Algorithm Demo compares four commonly-used sorting algorithms in a unique way: by showing them in action. Watch as each of these four algorithms performs exactly the same task in very different ways and with varying efficiencies.

How could tools like The Sorting Algorithm Demo be designed for cheminformatics? For example, finding a good way to visually compare different subgraph isomorphism algorithms, as applied to cheminformatics, could be an interesting problem in itself. This kind of visualization might even lead to insights into fundamentally different ways of approaching the problem. The same considerations could apply to other areas of cheminformatics such as 2-D structure layout or the calculation of descriptors.