Instead of developing custom visualization toolkits for specific data sets, the scientific data visualization community is heading towards web-based technologies to utilize actively developed visualization toolkits such as mpld3 (Ĩ is one of the most popular toolkits for creating custom interactive visualizations. For networks, dynamic features, such as zoom or pan, are particularly important because size of all but trivial networks requires such dynamic features to perform meaningful analysis. It is hard to perform exploratory data analysis only with static images, especially for large data sets, because some of the details are lost due to the limited size of printed papers or computer screens. Traditionally, analysis and visualization of biological data is done by desktop applications, and in most cases, visualizations created by popular libraries (e.g., matplotlibħ) are static images. Public biological data repositories are still growing rapidly and the demand for visualizing those complex biological data sets is high. Although Cytoscape and Cytoscape.js share some of the core concepts, such as Visual Styles or automatic layouts, they are completely independent software packages and there has been no simple way to use Cytoscape data sets in Cytoscape.js. Utilizing HTML5 and other emerging web technologies, the Cytoscape Consortium developed a JavaScript library for network visualization called cytoscape.js (ĥ, to meet the demand from the Cytoscape user community. Cytoscape is still an important platform for biological network data integration and analysis, but for data visualization and sharing, we need a new method to take advantage of modern web technologies. However, since they were designed before the re-discovery of AjaxĤ, and JavaScript technology was not mature enough to visualize large scientific data sets at the time, developers could not predict the success of JavaScript and related web technologies today. Around 2005, Java was one of the dominant programming languages for data visualization applications, and many Java-based feature-rich toolkits were developedģ. Today, it is a de-facto standard application for biological network analysis and visualization. Cytoscape was born as a GUI-based, Java desktop application in 2003Ģ.
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