Identify what makes the application successful In keeping with our long-standing commitment to our users and community-based software development, we discuss the principles that guide our process, design choices, and the decision to build the new “Cytoscape Home” software publication portal as part of the project. Here, we use Cytoscape as a case study to present six principles of our development approach to transition a mature bioinformatics software system to one that spans both the desktop and the web. The transition of the Cytoscape desktop application to a web-based application presents a unique set of challenges, as the functionality of Cytoscape is fundamentally different from existing web-based network analysis tools. But the web also challenges tool developers to find ways to best harness the distinct capabilities of desktop and web environments. Today, the increasing power and sophistication of web technologies have provided us, and many other bioinformatics software developers, opportunities to extend the impact of our tools through an integrated web-based ecosystem. By accessing applications on the web, users are free from the constraints imposed by their hardware and operating systems and from the inconvenience of carrying their work material from one computer to another. In recent years, the web has become a popular alternative to access applications and services as compared to local systems. Since its inception in 2001, the Cytoscape desktop application has served as a standard tool in academia and industry, and as such, it is downloaded about 300,000 times each year. Cytoscape ( Shannon et al., 2003 Smoot et al., 2011) is an open-source bioinformatics environment for the analysis, integration, visualization, and query of biological networks.
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