LMU Symposium 2017 Abstract: Samdarshi et al.

Improved data interoperability for GRNsight: a web application for visualizing models of gene regulatory networks

Mihir Samdarshi, Yeon-Soo Shin, Edward Bachoura, Eileen Choe, Nicole Anguiano, Anindita Varshneya, John David N. Dionisio, and Kam D. Dahlquist​

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 imports data from an adjacency matrix in an Excel workbook, then produces weighted or unweighted network graphs by representing genes as nodes and regulatory connections as edges, with colors, end markers, and thicknesses corresponding to the sign and magnitude of activation or repression. GRNsight visualizations can be modified through manually dragging nodes or adjusting sliders that change the force graph parameters. GRNsight follows open source and test-driven development best practices. The exhaustive testing framework consists of over 160 automated unit tests to ensure that the program is running as expected. To increase data interoperability, new input and export file types are accepted and produced by GRNsight, including Simple Interaction Format (SIF) text files and GraphML XML files. The addition of these file types required the refactoring of the test suite, separating syntactic tests for the different file formats from semantic tests that apply to all files. Consequently, there is more complete error and warning message coverage across different file types, providing valuable feedback to the user. 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.