Barry Demchak

NDEx, the Network Data Exchange.

Published in Cell Systems

The Cytoscape app article collection.

Published in F1000Research

As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online "cookbook" for app developers. This article collection is another resource to help res...

The anatomy of successful computational biology software.

Published in Nature Biotechnology

cyNeo4j: connecting Neo4j and Cytoscape.

Published in Bioinformatics

Cytoscape: the network visualization tool for GenomeSpace workflows.

Published in F1000Research

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 n...

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

Published in F1000Research

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape t...

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

Published in Nature Methods

Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources...

Biological network exploration with Cytoscape 3.

Published in Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]

Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental dat...

Porting and using PanGIA for Cytoscape 3: challenges and solutions.

Published in F1000Research

Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytosc...

NeXO Web: the NeXO ontology database and visualization platform.

Published in Nucleic Acids Research

The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hie...