2018 Undergraduate Research Symposium: Mihir Samdarshi

Data Comparison Features and Development Tool Improvements for GRNsight: a web app for visualizing gene regulatory networks

GRNsight is a web application and service for visualizing small- to medium-scale gene regulatory networks (GRNs). A GRN consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. GRNsight accepts input files in the Excel, SIF, and GraphML formats and then produces weighted or unweighted network graphs by representing genes as nodes and regulatory connections as edges. Activation is represented with magenta edges, repression is represented with cyan edges, and weight magnitudes below a certain threshold are represented with gray edges to denote weak activation or repression relationships. To better assess the relative strengths of the regulatory relationships, we added a slider that will adjust the gray threshold based on the magnitude of the weight. To facilitate comparison of graphs with different ranges of weight magnitudes, we added the ability to adjust weight normalization factors that control the thicknesses of the edges. Under the hood, the testing framework was refactored into semantic vs. syntactic tests of the validity of input files. Our development tool chain now also includes automatic test coverage calculation (currently 79%), linting for improved code style and readability, and continuous integration for quality assurance. Underlying third-party software libraries including Express, Node-XLSX, and D3 were updated to maintain compatibility and take advantage of new features. GRNsight is freely available at http://dondi.github.io/GRNsight/; the code is available under the open source BSD license at https://github.com/dondi/GRNsight.

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