The number of extensions has grown to 67 (from 15 for our initial publication), many of which are popular network layout algorithms.Īnyone is free to make a Cytoscape.js extension, and these can immediately be used in projects, as there is no approval process required. layouts), and they can also be used to add reusable user interface elements to Cytoscape.js network visualizations. They enable anyone to make additions to the application programming interface (API) of Cytoscape.js (e.g. 2.4 ExtensionsĮxtensions are a key component of Cytoscape.js. Finally, we have made many improvements to the styling that Cytoscape.js supports, with more than double the number of supported style properties as compared to the initial publication-enabling users to be more expressive with their networks. ES module support and console warning messages to mitigate issues early). We have improved our developer documentation based on feedback, including developer tool support (e.g. iterators) make it easier to integrate Cytoscape.js with modern JavaScript. Support for standard web frameworks, such as React ( ), eases the burden of integration of Cytoscape.js into new projects and integrations into standard web technologies (e.g. We have also added several new network layouts, such as ELK and Dagre ( and ). easier, precise node and edge selection in dense networks). Since the initial publication, improvements have been made to the usability of gestures (e.g. Usability is one of the most important priorities of Cytoscape.js, focusing both on app end-users and app authors. To minimize the effort required for upgrading from version 2 to version 3, we published an upgrade guide with a summarized list of all of the changes in version 3 as well as explicit instructions and examples for accommodating each change ( ). Additionally, we made changes to the API based on our experience with version 2 and based on feedback that we received from version 2 users. Breaking changes were also made in version 3 to enable improvements that would help users to avoid making common coding errors. These incompatibilities were made in version 3 in order to provide integrations with current browser technology standards, such as the ECMAScript (ES) 2015+ specifications. Since then, we have released version 3, which breaks with some of the conventions of version 2. The initial publication of Cytoscape.js described version 2 of the software. Cytoscape.js has consistently accelerated its adoption rate, with exponential growth of year-over-year user installations, since its initial publication in 2015 ( ). ![]() bug reports), and it provides a predictable and timely framework that the community can use when making third-party contributions. This release schedule gives users a quick turnaround time for feedback (e.g. Similarly, a feature release is published if new features have been added during that month. Each week, a patch release is made if there are any bug fixes that have been made in the previous week. We currently use a weekly cadence for patch releases and a monthly cadence for feature releases. Overall, Cytoscape.js has had 226 software versions published, with 177 of them made after the initial publication ( Franz et al., 2016). 2 Implementation updates 2.1 Releases and user adoption Here, we provide an overview of the improvements and additions to Cytoscape.js since its original publication ( Franz et al., 2016), including details about releases, user adoption, major updates in version 3, performance, usability improvements, extensions and example use cases. Ensembl, FlyBase and WormBase) ( Drysdale, 2008 Harris et al., 2010 Howe et al., 2021), governmental organizations and commercial organizations ( and ). Cytoscape.js is used by research groups (e.g. On GitHub, the most widely used platform for distributing open-source projects, Cytoscape.js is in the top 0.01% of software packages by popularity measured by number of user stars. used to store protein–protein interaction network data. to create exploratory interactive visualizations in web applications (apps), and as a data representation, e.g. ![]() Cytoscape.js is used in research both as a tool, e.g. It is a critical software component used in research fields such as biology, sociology, computer security, cloud computing and data science. Cytoscape.js is a technology that can be embedded within web-apps, websites and servers that enable users to interact with networks for visualization and analysis.
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