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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