SURP 2015 Abstract

Test-Driven Development Improves GRNsight: a Web Application for Visualizing Models of Gene Regulatory Networks

Anindita Varshneya, Nicole A. Anguiano, 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. GRNsight automatically lays out the network graph based on GRNmap output spreadsheets. GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (activation or repression) and magnitude of the GRNmap weight parameter. Visualizations can be modified through manual node dragging and sliders that adjust the force graph parameters. We have now implemented an exhaustive unit testing framework using Mocha and the Chai assertion library to perform test-driven development where unit tests are written before new functionality is coded. This framework consists of over 140 automated unit tests that examine 450 test files to ensure that the program is running as expected. Error and warning messages have a three-part framework that informs the user what happened, the source of the problem, and possible solutions. For example, GRNsight returns an error when the spreadsheet is formatted incorrectly or the maximum number of nodes or edges is exceeded. The completion of the testing framework marks the close of development for version 1 (the current release stands at version 1.12). New features will be developed for GRNsight version 2.0. GRNsight is available at http://dondi.github.io/GRNsight/.

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