Software Tools for Systems Biology: Visualizing the Outcomes of N Experiments on M Entities

Systems biology deals with genes, proteins, ions and other molecular entities. It involves the integrated analysis of these molecular entities from many experiments conducted under different conditions. This common feature - many treatment conditions and thousands or more entities - poses a challenge to finding the answers to natural questions such as: Which subsets of conditions yield similar outcomes? Which entities respond similarly in many conditions? and Which functional groupings of entities are most affected by which conditions? In this chapter, we describe a visualization tool to help answer these questions, complementary informatic tools to support alternate visualizations, and explore the lessons learned in constructing that tool both fromthe software designer's and biologist's perspective.