Mathematica's Computable Document Format (CDF) Player: a Versatile Tool for Displaying Interactive Graphs and 3‐D Structures

Considering that biochemical research often aims to establish structure/function correlations, biochemistry students need exposure to the methodology biochemists use for analyzing biomolecular structures and their functions. The free Jmol web browser plug‐in is particularly effective as a molecular visualization tool for introducing students to interactive structure exploration but the options for engaging students in functional analysis are limited. For example, interactive data plots promote student understanding of biochemical reactions but existing computer applications tend to be technically cumbersome and/or expensive. A notable exception is the computable document format (CDF) player, a web browser plugin designed to “play” content or “notebooks” created with Wolfram's Mathematica 8 program. Although Mathematica requires certain programming sophistication, notebooks, once created, can be readily disseminated online with the free CDF player. As described with this poster, we have created a series of interactive CDF plots that aim to facilitate student understanding and exploration of various types of reactions typically encountered in a biochemistry course. In addition, we evaluate the new 3‐D molecular rendering capability of Mathematica, which provides an interesting alternative for projecting interactive PDB‐based structures with a web browser.