Cytoscape: the network visualization tool for GenomeSpace workflows

Abstract

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

Cited by papers we hold 3

• Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes · 2019
  Corrected
• A human gut phage catalog correlates the gut phageome with type 2 diabetes · 2018
  No notice
• The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease · 2015
  No notice

Questions about this paper

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.