The 2004 Annual Meeting of the Society for Mathematical Biology
University of Michigan
Society for Mathematical Biology
July 24, 2004 - July 28, 2004
Systems Biology Education: Exploring Complex Networks in DNA Microarrays and Metabolonomics with BioGrapher and JavaBENZER
J. R. Jungck, R. Viswanathan, V. Streif, D. Beck; Biology, Beloit College, Beloit, WI, Chemistry, Beloit College, Beloit, WI
Biology has come of age as a mature discipline that integrates biology, mathematics, computer science, and engineering. It is vital to comprehending the strong interconnectedness of biological components at the intra- and intercellular levels. However, undergraduate biology students usually find it difficult to obtain the level of sophistication in requisite mathematical concepts and tools - graph theory, matrix algebra, cluster necessary to understand connectivity. We describe two software tools - BioGrapher and JavaBENZER - that we have developed and used in classes that serve as both a programmatic and visual front end for graph theoretical analyses, which in turn allows students to easily pose and solve problems using large real world data sets available from DNA microarray experiments on cellular pathways. Specifically, BioGrapher is an Excel application that allows students to import data from the web, e.g., Kyoto Encyclopedia of Genes and Genomes, to use sophisticated ActiveX controls embedded in the spreadsheet to call upon Tom Sawyer Graph Layout tools: circular, orthogonal, symmetric, and hierarchical, that easily show clustering and connectivity relationships, each in an often unique and complementary fashion. Such tools are especially helpful in visualizing systematic patterns of up- and down-regulated expression of genes. JavaBENZER, a tool specifically designed to handle interval graphs such as employed to assemble DNA contigs and protein fragments into full sequences, deploys symmetric matrix manipulation to identify ordered maximal cliques. JavaBENZER , an upgrade from BENZER (Jungck et al., 2001), seamlessly works with BioGrapher. The power of two programs will be illustrated by demonstrating the reanalysis of data in published papers on signaling pathways.
BioQUEST Staff Attending: