SURP 2015 Abstract

Nicole A. Anguiano, Anindita Varshneya, 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

GRNsight is a web application and service for visualizing models of gene regulatory networks (GRN). A gene regulatory network consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. GRNmap, a MATLAB program that performs parameter estimation and forward simulation of a differential equations model of a GRN, can mathematically model GRNs. The general graph visualization tools that exist for displaying GRNs did not fulfill our needs, so we created GRNsight. GRNsight automatically lays out the network graph based on spreadsheets uploaded from GRNmap. GRNsight colors the edges and adjusts their thicknesses based on the sign (activation or repression) and magnitude of the GRNmap weight parameter. GRNsight uses pointed and blunt arrowheads to indicate activation and repression, respectively. Visualizations can be modified through manual node dragging and sliders that adjust the force layout parameters. Since version 1.0, GRNsight has acquired significant user interface improvements, bug fixes, extended robustness to errors, and aesthetic refinements. Demo spreadsheets are now available for users who do not have their own models. An exhaustive unit testing framework was implemented using Mocha and Chai assertion library in order to minimize unforeseen issues with functionality updates. This framework exists of over 450 test sheets and 150 unit tests that ensure that the program is running as expected, and catches any errors that a user created sheet may have. GRNsight's current release is version 1.10, with beta version 1.11 available for testing new features. GRNsight is available at http://dondi.github.io/GRNsight/.