NRNB and Cytoscape

Introduction to the National Resource for Network Biology

How to Cite Cytoscape

Cytoscape project needs your support! Please cite either of the following papers when you use Cytoscape in your publications, which is very important to sustain our federal funding.

Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T.

A travel guide to Cytoscape plugins

Nature Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6.

[PubMed entry]

Michael Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker

Cytoscape 2.8: new features for data integration and network visualization

Bioinformatics. 2011 February 1; 27(3): 431–432.Published online 2010 December 12.

[PubMed entry]

Melissa S Cline, Michael Smoot, Ethan Cerami, Allan Kuchinsky, et al.

Integration of biological networks and gene expression data using Cytoscape

Nature Protocols 2, 2366 - 2382 (2007) Published online: 27 September 2007 | doi:10.1038/nprot.2007.324

[PubMed entry]

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Genome Research 2003 Nov; 13(11):2498-504

[Abstract] [PDF] [PubMed entry]

What Can You Do With Cytoscape?

Biology

Cytoscape supports many use cases in molecular and systems biology, genomics, and proteomics:

Load molecular and genetic interaction data sets in many standards formats
Project and integrate global datasets and functional annotations
Establish powerful visual mappings across these data
Perform advanced analysis and modeling using Cytoscape Apps
Visualize and analyze human-curated pathway datasets such as WikiPathways, Reactome, and KEGG.

Social Science

Cytoscape is used by social scientists to:

Visualize and analyze large social networks of interpersonal relationships
Assemble social networks from tables and forms
Gather social interactions from the web by variety of web service APIs with scripting languages and save it in standard data file formats. Cytoscape supports most of the standard file formats .
Calculate network statistics using Apps
Use with other tools, such as R with sna/ igraph package or NetworkX, for more advanced analysis

Semantic Web

Cytoscape is also a tool of choice for the semantic web community, since the semantic web is encoded and viewed as a network of knowledge and resources.

Load and visualize Resource Description Framework (RDF) data as networks
Import data from Triplestore through simple text table or XML-RDF
Query RDF data by SPARQL
Perform reasoning by apps
Platform to develop custom semantic web applications with other semantic web frameworks including Jena and Sesame

General Complex Network Analysis

Cytoscape is domain-independent and therefore is a powerful tool for complex network analysis in general.

Calculate statistics for networks by Apps such as NetworkAnalyzer or CentiScaPe
Find shortest path
Find clusters by various kinds of algorithms
Use with other tools for more advanced analysis
Perform advanced network analysis in popular tools, including igraph, Pajek, or GraphViz and import it to Cytoscape as standard file formats like GraphML

App Development

Cytoscape is expandable and extensible. Cytoscape has a vibrant App developer community and over a hundred Apps developed by third parties.

Source code is available on GitHub
Running on OSGi framework
Develop simple and complex Apps in Java
Clean, Rich Cytoscape Application Programming Interface ( API)
Active developer community
Write simple functions with scripting languages, including Ruby, Python, Groovy, and JavaScript

Network Data Integration, Analysis, and Visualization in a Box

Learning Cytoscape

NRNB and Cytoscape

How to Cite Cytoscape

What Can You Do With Cytoscape?

Biology

Social Science

Semantic Web

General Complex Network Analysis

App Development

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