Note that the GenomeSpace app makes the GenomeSpace file system available to Cytoscape even without the user first executing the GenomeSpace web application. Each menu item enables the user to navigate within the file system using a chooser. To facilitate this, GenomeSpace also allows the user to identify a GenomeSpace-stored Cytoscape session file (.cys) while launching Cytoscape, thereby facilitating a seamless tool launch.Īdditionally, the app adds menu items to Cytoscape to enable loading or saving a Cytoscape session, a network, or node or edge attributes in the GenomeSpace file system from within Cytoscape. From the Cytoscape perspective, genomic data can come from numerous sources and can be rendered to numerous destinations, where the GenomeSpace file system can be a source, a destination, or both. The GenomeSpace app enables Cytoscape to act as a tool in a workflow executed within the GenomeSpace web application. Within this paper, we discuss only the “Cytoscape 3” tool, and refer to it simply as “Cytoscape”. Its “Cytoscape” refers to the deprecated Cytoscape version 2, and its “Cytoscape 3” refers to Cytoscape version 3, which is the currently released version ( ). Note that GenomeSpace supports two Cytoscape tools it calls “Cytoscape” and “Cytoscape 3”. We also describe Cytoscape’s GenomeSpace app, how its user interface adds GenomeSpace functionality within Cytoscape, and how it uses GenomeSpace’s Client Development Kit (CDK) to access the GenomeSpace file system to read input files or write result files. In this paper, we describe a specialized launch strategy that addresses this. Paradoxically, Java-based tools (such as Cytoscape) run directly on the user’s workstation instead of within a browser. To launch a tool, GenomeSpace opens a new browser page using a URL specific to the tool. Cytoscape distinguishes itself by being graph-oriented and delivering rich filtering, layout, and visual style features backed up by an extensive collection of third-party apps 10, including pathway analysis, data integration, GO annotation, and more. GenomeSpace offers a short list of tools that enable network visualization and analysis, including Cytoscape, Genomica ( ) (for module network trees), Gitools 6 (for heat maps), and IGV 9 (for sequencing data). By tying these features together, GenomeSpace provides a comprehensive and effective environment for genomic research. While some tools implement specific and constrained functionality (e.g., ISAcreator 4), others are complex and rich applications (e.g., GenePattern 5, Gitools 6, and Cistrome 7), and yet others are fully featured workflow management systems themselves (e.g., Galaxy and Sage Synapse 8). While there exists a number of workflow engines that can perform biological analyses (e.g., Taverna 1, BioKepler 2, and Galaxy 3), GenomeSpace distinguishes itself by combining a collaboration-oriented file system (incorporating sharing and stored metadata), a robust and user-extensible spectrum of genomic tools, and a library of recipes demonstrating best practices for the orchestration of GenomeSpace tools to achieve common and important bioinformatic results. It focuses on critical design issues for the app, and gives a brief app demonstration highlighting the resulting user interface and data transfer functionality. This paper describes Cytoscape’s GenomeSpace app, which links GenomeSpace and Cytoscape, thereby enabling data to flow between Cytoscape and other GenomeSpace tools. Cytoscape is a standalone desktop application that enables users to analyze, visualize, and publish complex networks – with its GenomeSpace app (“the app”, ), it doubles as a tool available to GenomeSpace workflows. The data and results from a given tool are stored by GenomeSpace as private, public, or shared files that are made available to other tools in the workspace. It hosts a variety of third party tools that it can launch to perform queries of public genomic databases, customized analyses, and customized visualization and publishing. GenomeSpace is a web-based application ( ) that provides a workspace environment for executing biologic analysis workflows involving genomic data.
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