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Osprey: A Network Visualization System

DOI: 10.1186/gb-2002-3-12-preprint0012

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Abstract:

The rapidly expanding biological datasets of physical, genetic and functional interactions present a daunting task for data visualization and evaluation [1]. Existing applications such as Pajek allow the user to visualize networks in a simple graphical format [2], but lack the necessary features needed for functional assessment and comparative analysis between datasets. Typically, interaction networks are viewed within a graphing application, but data is manipulated in other contexts, often manually.To address these shortfalls, we developed a network visualization system called Osprey that not only represents interactions in a flexible and rapidly expandable graphical format, but also provides options for functional comparisons between datasets. Osprey was developed with the Sun Microsystems Java Standard Development Kit version 1.4.0_02 [3], which allows it to be used both in standalone form and as an add-on viewer for online interaction databases.Osprey represents genes as nodes and interactions as edges between nodes (Figure 1). Unlike other applications, Osprey is fully customizable and allows the user to define personal settings for generation of interaction networks, as described below. Any interaction dataset can be loaded into Osprey using one of several standard file formats, or by upload from an underlying interaction database. By default, Osprey uses The General Repository for Interaction Datasets as a database (The GRID; http://biodata.mshri.on.ca/grid webcite), from which the user can rapidly build out interaction networks. User-defined interactions are added or subtracted from mouse-over pop-up windows that link to the database. Networks can be saved as tab delimited text files for future manipulation or exported as Joint Photographic Experts Group (JPEG or JPG) graphics, Portable Network Graphics (PNG), and Scalable Vector Graphics (SVG) [4]. The SVG image format allows the user to produce high quality images that can be opened into applications such

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