RHandler is an abstract Java class that is extended by RserveHandler and RCallerHandler classes that add support to Rserve and RCaller libraries, respectively. Within the grey box the class hierarchy of the classes responsible for establishing the connection between Cytoscape and R is represented. Diagram of the Cyrface interaction layer with R. RHandler that contains the signature of all the necessary methods to establish and maintain a connection withįigure 1 depicts the hierarchical structure of these classes and the connection points between these two different environments. RCallerHandler Java classes, respectively. Rserve is currently being used by several mature projects, among them the TCP/IP server allowing other programs from various languages to connect to an R session and access its features. On the one hand, to support the communication between Interaction between these two different environments (invoking ImplementationĬyrface is a Java open-source framework developed to establish the connection between Finally, we discuss on-going and future developments. Then, to illustrate the usefulness of Cyrface, we show two existing apps, CytoCopteRġ1, that make use of Cyrface, and we demonstrate an implementation of a simplified version of theĭataRail 12 workflow. This paper is structured as follows: Firstly, we provide a description of the implementation of Cyrface. RCytoscape would be to handle experimental data from Java, whereas Cyrface allows a connection from Java to The fundamental difference between RCytoscape and Cyrface is that RCytoscape supports the connection from It is aīioconductor R package that establishes a connection between RCytoscape 9 is another tool that exists to link R and Cytoscape. R within a different environment with complementary features. Thus, Cyrface complements Taverna and Galaxy by enhancing GUIs for Galaxy is an open-source web-platform to assemble workflows based on genomic experimental data analysis. Java open-source tool for the general development and execution of workflows. By linking these two environments,Ĭyrface allows one to use Cytoscape as a graphical user interface forĬytoscape apps to access the wealth of methods implemented inĨ can call R packages from a graphical user interface (GUI)-based interface. 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.Ĭytoscape that facilitates an interface between anyĬyrface is designed to integrate the major strengths ofĬytoscape environments by providing a general 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. Therefore, the use of intuitive graphical interfaces that simplifies their use can enhance the usability of these R packages.Ĥ is a Java open-source framework with an intuitive graphical interface devoted to the visualization and analysis of networks. R and using its packages can be a time consuming task. 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 These packages are subject to stringent quality control in terms of functionality and documentation. Furthermore,īioconductor 2 provides a large collection of curated packages to analyse biological data developed in 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 The availability of high-throughput experimental data has led to the development of multiple computational methods to analyse these data.
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