Fuzzy modeling of metabolic maps in MetNetDB

Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and visualize due to the diverse types of information that need to be represented. FCModeler, a publicly available software package is designed to enable the biologist to visualize and model metabolic and regulatory network maps in plants. It links to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases and input from biologists in their area of expertise. FCModeler evaluates hypotheses and provides a graph-theoretic modeling framework for assessing the large amounts of data captured by high-throughput gene expression experiments. This leads to a new method for classifying gene expression data by combining network, gene ontology, and measured expression information in a fuzzy clustering framework.