Presentation Title

Improved Visual Performance and Enhanced Test Files for Different File Formats for GRNsight: a Web Application for Visualizing Models of Gene Regulatory Networks

Faculty Mentor

John David N. Dionisio, Kam D. Dahlquist, Ben G. Fitzpatrick

Start Date

18-11-2017 12:30 PM

End Date

18-11-2017 1:30 PM

Location

BSC-Ursa Minor 96

Session

Poster 2

Type of Presentation

Poster

Subject Area

engineering_computer_science

Abstract

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 either an Excel workbook or a SIF or GraphML file, 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. Previous visual issues regarding edge thickness have been adjusted along with corresponding test files to check for any visually unappealing faults. The new GRNsight graph now displays self-regulatory arrows with consistent positions regardless of the node size, edge thickness, or whether it’s weighted. On the server side, syntactic tests for the importable GraphML File Format (.graphml) were written, which return end user-targeted error messages to the user if an incorrectly formatted GraphML file is imported into GRNsight. 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 runs as expected. We are currently working on changing the embedded D3 code from version 3 to version 4 and planning on applying this for the future release. 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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Nov 18th, 12:30 PM Nov 18th, 1:30 PM

Improved Visual Performance and Enhanced Test Files for Different File Formats for GRNsight: a Web Application for Visualizing Models of Gene Regulatory Networks

BSC-Ursa Minor 96

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 either an Excel workbook or a SIF or GraphML file, 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. Previous visual issues regarding edge thickness have been adjusted along with corresponding test files to check for any visually unappealing faults. The new GRNsight graph now displays self-regulatory arrows with consistent positions regardless of the node size, edge thickness, or whether it’s weighted. On the server side, syntactic tests for the importable GraphML File Format (.graphml) were written, which return end user-targeted error messages to the user if an incorrectly formatted GraphML file is imported into GRNsight. 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 runs as expected. We are currently working on changing the embedded D3 code from version 3 to version 4 and planning on applying this for the future release. 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.