Java Treeview—extensible visualization of microarray data

Concepts

ComputingBioinformaticsVisualizationData VisualizationGenomic Data AnalysisScientific VisualizationGenomic Data VisualizationHigh-dimensional Data VisualizationVisual Analytics For Scientific DataVisual Data ExplorationFile Format DocumentationFile Format ManagementMicroarray Analysis

TL;DR

Open‑source software promotes innovation by enabling users to extend existing applications, yet the popular microarray visualization tool Treeview is closed‑source and platform‑specific, limiting its utility and extensibility. Java Treeview is an open‑source, cross‑platform rewrite designed to handle very large datasets and support file‑format extensions for visualizing and comparing additional analysis results. It is implemented as a cross‑platform Java applet that handles large datasets, supports file‑format extensions, and can be embedded on any website without server‑side setup. Its general file format and open‑source nature make Java Treeview an attractive solution for a broad class of visualization problems.

Abstract

Open source software encourages innovation by allowing users to extend the functionality of existing applications. Treeview is a popular application for the visualization of microarray data, but is closed-source and platform-specific, which limits both its current utility and suitability as a platform for further development. Java Treeview is an open-source, cross-platform rewrite that handles very large datasets well, and supports extensions to the file format that allow the results of additional analysis to be visualized and compared. The combination of a general file format and open source makes Java Treeview an attractive choice for solving a class of visualization problems. An applet version is also available that can be used on any website with no special server-side setup.