SURP 2015 Abstract Trixie Roque and Tessa Morris

Trixie Anne M. Roque, Tessa A. Morris, Kam D. Dahlquist, John David N. Dionisio, and Ben G. Fitzpatrick

Department of Electrical Engineering & Computer Science, Department of Biology, Department of Mathematics, Loyola Marymount University, 1 LMU Drive, Los Angeles, CA 90045 USA

Test-Driven Development and Functionality Improvements to GRNmap, a Gene Regulatory Network Modeling Application

A gene regulatory network (GRN) consists of a set of transcription factors that regulate the level of gene expression encoding other transcription factors. The dynamics of a GRN is how gene expression in the network changes over time. GRNmap is a complex MATLAB software package that uses ordinary differential equations to model the dynamics of medium-scale GRNs from budding yeast, Saccharomyces cerevisiae. The program estimates production rates, expression thresholds, and regulatory weights for each transcription factor in the network based on DNA microarray data, and then performs a forward simulation of the network dynamics. Since v1.0, we have made design changes, added new features, fixed bugs, implemented testing a framework, and created documentation. For example, GRNmap now accepts and outputs Excel worksheets with more descriptive names, computes the standard deviations of the log2 expression data, and outputs an optimization diagnostics sheet which includes both actual and minimum least squares error. We have also designed sixteen manual input sheet tests to uncover and fix bugs. We incorporated these tests into an automated testing framework that will speed debugging and prevent future code regressions. We have added documentation to our website and wiki and constructed a UML activity diagram to document the program's overall flow and how each function processes information. The source code and executable (which contain demo files and can run without a MATLAB license) for the updated version 1.2 are available for download at http://kdahlquist.github.io/GRNmap/ under the BSD open source license.