GRNsight
From Bioinformatics.Org Wiki
Contents |
Description
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 the dynamics of 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 135 automated unit tests that examine about 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. In version 2.0 of GRNsight, a new feature will be implemented that colors the nodes (genes) based on the expression data. The user will have the choice to display the experimental data or the data produced by the forward simulation feature in GRNmap. GRNsight is available at http://dondi.github.io/GRNsight/.
Home page
Source code
Supported platforms
- GRNsight has been tested with and confirmed to be working in Chrome version 43.0.2357.65 or higher and Firefox version 38.0.1 or higher on Windows 7 and Mac OS X operating systems. It may not work with other browsers, versions, or operating systems.
Documentation
- Documentation page
- Wiki
- Posters and presentations on SlideShare.
