![]() ![]() For the user, Cyni apps and their parameters are accessible via the Cyni GUI panel within Cytoscape. Like Cytoscape and its apps, Cyni and its apps are written in Java to allow easy portability to all common operating systems. Cyni comprises app implementations of commonly used pairwise score functions (metrics), data discretization and data imputation, network inference, along with configurable graphical user interfaces (GUIs), API and common data structures. The Cyni framework provides support for network inference through an extensible system of Cytoscape apps that provide key functionality in and around network inference, while eliminating the need for interaction with the much more complex Cytoscape application programmer interface (API Fig. Here, we describe the structure of Cyni, and illustrate the implementation of the ARACNE network inference method ( Margolin et al., 2006), which has confirmed MYC as a major regulatory hub in human B cells, and identified a number of new MYC targets ( Basso et al., 2005). CYTOSCAPE NETWORKS CODETo stimulate the exchange between the network inference and biomedical research communities, we have developed the open-source computational framework Cyni that allows to rapidly transform Java-based network inference core code into interactive components (apps) of the Cytoscape visualization and analysis platform ( Cline et al., 2007 Shannon et al., 2003), and thereby to rapidly make novel methods accessible to a large community of biomedical researchers. However, the use and adoption of these methods in biomedical research has been slow. Perhaps for this reason the development of methods that infer networks from transcriptomics or other global molecular measurements has recently received much attention ( Marbach et al., 2012 Poultney et al., 2012). In contrast, the experimental measurement of component interactions-important for analyses in a network context-is still far more difficult. The availability of large-scale experimental technologies has enabled the routine measurement of global abundances and states of molecular components in cellular systems. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app.Īvailability and implementation: Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Here, we present Cyni, an open-source ‘fill-in-the-algorithm’ framework that provides common network inference functionality and user interface elements. 1.2.3), run npm version 1.2.3.Motivation: Research on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. For a breaking API change, run npm version major.For a new feature release, run npm version minor. CYTOSCAPE NETWORKS PATCHFor a bug fix / patch release, run npm version patch.The version command in npm updates both package.json and git tags, but note that it uses a v prefix on the tags (e.g. Bump the version number with npm version, in accordance with semver.Make sure the linting is passing: npm run lint.Make sure the tests are passing: npm test. CYTOSCAPE NETWORKS INSTALLYou can npm test to run all tests, or you can run mocha -g specific-test-name (prerequisite: npm install -g mocha) to run specific tests.Ĭhai is included to make the tests easier to read and write.
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