Taverna is a standalone Java open-source tool for the general development and execution of workflows. Workflow management systems such as Taverna 5 and Galaxy 6– 8 can call R packages from a graphical user interface (GUI)-based interface. It also enables Cytoscape apps to access the wealth of methods implemented in R.
By linking these two environments, Cyrface allows one to use Cytoscape as a graphical user interface for R packages. Cyrface is designed to integrate the major strengths of R and Cytoscape environments by providing a general Java to R interface. Here, we present Cyrface, an app for Cytoscape that facilitates an interface between any R package and Cytoscape. These user defined extensions are termed plug-ins (1.x and 2.x) or apps (3.x) depending of which version of Cytoscape is being used. It is arguably one of the most used tools in bioinformatics, and has a variety of user developed extensions to solve numerous computational biology problems. Cytoscape 3, 4 is a Java open-source framework with an intuitive graphical interface devoted to the visualization and analysis of networks. Therefore, the use of intuitive graphical interfaces that simplifies their use can enhance the usability of these R packages.
#CYTOSCAPE 3 TUTORIAL SOFTWARE#
It is an open-source project hosting 824 active and curated software packages as of May 2014.įor those not familiar with computational programming, learning R and using its packages can be a time consuming task. These packages are subject to stringent quality control in terms of functionality and documentation.
Furthermore, Bioconductor 2 provides a large collection of curated packages to analyse biological data developed in R.
#CYTOSCAPE 3 TUTORIAL ARCHIVE#
Multiple R packages for computational biology and bioinformatics are available in various resources such as the Comprehensive R Archive Network (CRAN). One of the most used environments is the statistical programming language R 1. The availability of high-throughput experimental data has led to the development of multiple computational methods to analyse these data.
#CYTOSCAPE 3 TUTORIAL DOWNLOAD#
Download links, installation instructions and user guides can be accessed from the Cyrface’s homepage ( ) and from the Cytoscape app store ( ). Cyrface’s utility has been demonstrated for two Bioconductor packages ( CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. There is an increasing number of software packages to analyse biological experimental data in the R environment.
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