An Expression Database for Node Coloring on GRNsight: a web application for visualizing models of gene regulatory networks

Date of Completion


Degree Type

Honors Thesis


Computer Science (CMSI)

First Advisor

John David N. Dionisio

Second Advisor

Kam Dahlquist


GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). 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. Using a GRNmap output workbook, GRNsight automatically visualizes the network as a graph. GRNsight uses the model output to color-code the edges based on the activation and repression relationships between the transcription factors and colors the nodes based on time course gene expression data. We have added a feature to store expression data in a database, so that users of GRNsight can view and interact with already-existing expression data pulled from the Dahlquist lab and other publicly available datasets. The database is hosted by Amazon Web Services (AWS) Relational Database Service (RDS) and uses a PostgreSQL engine, from which GRNsight performs dynamic queries in response to user requests. GRNsight is available at https://dondi.github.io/GRNsight/, and its code can be viewed at https://github.com/dondi/GRNsight.