Abstract
Summary: Ondex Web is a new web-based implementation of the network visualization and exploration tools from the Ondex data integration platform. New features such as context-sensitive menus and annotation tools provide users with intuitive ways to explore and manipulate the appearance of heterogeneous biological networks. Ondex Web is open source, written in Java and can be easily embedded into Web sites as an applet. Ondex Web supports loading data from a variety of network formats, such as XGMML, NWB, Pajek and OXL.Availability and implementation: http://ondex.rothamsted.ac.uk/OndexWeb.Contact: keywan.hassani-pak@rothamsted.ac.uk
Highlights
The integrative approach to systems biology studies the interactions between molecular or cellular components to understand how a behavior or phenotype might emerge from the properties or structure of the interactions
It is common in systems biology to adopt network formalisms to represent, visualize and explore interaction information, and a number of web-based applications are available for the visualization of biological networks (Gehlenborg et al, 2010)
We describe here a new implementation of the visualization software from the Ondex suite that enables integrated networks and associated quantitative data to be presented in a web browser. This enables delivery of results from pre-integrated datasets to end-users, as featured in the QTLNetMiner system, and overcomes the significant obstacle encountered by many biologists of installing
Summary
The integrative approach to systems biology studies the interactions between molecular or cellular components to understand how a behavior or phenotype might emerge from the properties or structure of the interactions. We describe here a new implementation of the visualization software from the Ondex suite that enables integrated networks and associated quantitative data to be presented in a web browser This enables delivery of results from pre-integrated datasets to end-users, as featured in the QTLNetMiner system (http:// ondex.rothamsted.ac.uk/QTLNetMiner/), and overcomes the significant obstacle encountered by many biologists of installing. Ondex Web has been built as a Java applet, reusing proven functions and plugins from the Ondex desktop application This results in a richer repertoire of functions for exploring and manipulating heterogeneous information networks (Sun and Han, 2012) than currently available in Cytoscape Web. Ondex Web provides new features not described before, including easy-to-use search functions for loaded data and across web services (e.g. ChEMBL, UniProtKB). Example data sets are available for download (http://ondex.org/doc.html)
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