Osprey: a network visualization system

By Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers. Genome Biology, 2003

517 citations recorded by the source corpus.

We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f793b0d5fc6bae999e6d37f8e7b481e312bd8be7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Trey Ideker
2. Gary D. Bader
3. Mike Tyers
4. Falk Schreiber
5. Lorrie Boucher
6. J. Walker
7. Frank Eisenhaber
8. Oliviero Carugo

Citations in the corpus

• VANTED: A system for advanced data analysis and visualization in the context of biological networks (2006, methodology): “There are a number of tools which facilitate the editing and visualization of biological networks, among them BioMiner [8], PaVESy [9], VisANT [39], Patika [7], and Osprey [40].”
• Data Mining Techniques for the Life Sciences (2010, methodology): “In addition to mirBase, there are several other online resources with similar features (miRNA sequences, target predictions, genomic tools, pathways) including Argonaute (37), miRNAmap (38), miRNApath (39), and miRGen (40).”
• BisoGenet: a new tool for gene network building, visualization and analysis (2010, methodology): “Several tools as Cytoscape[14,15], VisANT[16], Osprey [17] and Biological Networks[18], have being developed for reconstruction and visualization of networks of biological entities, for reviews see Pavlopoulos et al. [18] and Suderman et al[19,20].”
• Protein-to-protein interactions: Technologies, databases, and algorithms (2010, background): “Osprey25 [Breitkreutz et al. 2003] is a user-friendly network visual­ization system; but it lacks in analysis since it provides only basic .ltering capabili­ties.”
• Hive plots - rational approach to visualizing networks (2012, unknown): “Gephi [25], MatrixExplorer [26], Osprey [27] and”
• The BioGRID Interaction Database: 2008 update (2007, methodology): “Dataset manipulation was performed with the Osprey visualization system (10).”
• How to infer gene networks from expression profiles (2007, methodology): “In addition to reverse-engineering algorithms, network visualisation tools are available online to display the network surrounding a gene of interest by extracting information from the literature and experimental data sets, such as Cytoscape (Shannon et al , 2003)(http://www.cytoscape.org/features.p”
• Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…Workbench http://nwb.cns.iu.edu NWB Team, 2006 Ondex http://www.ondex.org Kohler et al., 2006 Osprey http://biodata.mshri.on.ca/osprey/servlet/Index Breitkreutz et al., 2003 Pajek http://pajek.imfm.si/doku.php Batagelj & Mrvar, 1998 PathDraw http://rospath.ewha.ac.kr/toolbox/PathwayViewerFrm.jsp…”
• Computational approaches in target identification and drug discovery (2016, methodology): “The Biological General Repository for Interaction Datasets (BioGRID)[30] is aninterac-tion repository with compiled biological data freely available in standardized formats, linked with software platforms for visualization of complex interaction networks such as Osprey [31] and Cytoscape [32].”
• BioGRID: a general repository for interaction datasets (2005, methodology): “A defining feature of the GRID data-base is an inter-dependent visualization tool called Osprey (http://biodata.mshri.on.ca/osprey) that runs as a desktop application in Windows, Linux and OSX environments (28).”
• What Color Is Your Jacobian? Graph Coloring for Computing Derivatives (2005, background): “) A related concept has been studied in the social and biological network literature as the k-core of a graph [21, 105].”
• The BioGRID Interaction Database: 2011 update (2010, methodology): “BioGRID interaction data can also be accessed automatically through biological network visualization applications that include Osprey (26), Cytoscape (27), GeneMania (28) and ProHits (29).”
• The BioGRID interaction database: 2013 update (2012, methodology): “BioGRID datasets can also be directly interrogated through network visualization and analysis suites, including the original Osprey viewer (43), Cytoscape (44) Nucleic Acids Research, 2013, Vol.”
• Integration of biological networks and gene expression data using Cytoscape (2007, methodology): “A number of software tools are available for network visualization and analysis, including Ospre”
• Network Visualization by Semantic Substrates (2006, background): “A third common strategy uses a circular layout for nodes that produces an elegant presentation with crisscrossing lines through the center of the circle ([22], [7]).”
• Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways (2004, methodology): “Interaction maps were created using the network visualization system Ospre”