Cytoscape 2.8.2

Cytoscape 2.8.2 supports custom graphics, functions, and commands.

Module Finding

Cytoscape supports nested network structure. You can easily visualize relationship of modules in the network.

Large Scale Data Visualization

With Cytoscape and modern workstations, you can handle large scale networks such as human interactome or social network datasets.

Custom Graphics 1

From Cytoscape 2.8.0, you can map up to nine images per node.

Custom Graphics 2

Mapping charts to node is one of the most common usecase of Custom Graphics. You can map charts generated web services such as Google Chart API.

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.

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, Nerius Landys, Chris Workman, Rowan Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers, Ruth Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere, John Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R Pico, Aditya Vailaya, Peng-Liang Wang, Annette Adler, Bruce R Conklin, Leroy Hood, Martin Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J Warner, Trey Ideker & Gary D Bader

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 formats
Project and integrate global datasets and functional annotations
Establish powerful visual mappings across these data
Perform advanced analysis and modeling using Cytoscape plugins
Visualize and analyze human-curated pathway datasets such as Reactome or 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 API and scripted web crawlers within Cytoscape
Calculate network statistics using plugins
Use with other tools, such as R with sna/ igraph package, 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 plugins
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 plugins such as NetworkAnalyzer or CentiScaPe
Find shortest path
Find clusters by various kinds of algorithms
Use with other tools for more advanced analysis
Import data files from other popular network analysis tools, including igraph, Pajek, and GraphViz (by standard file formats like GML)

Plugin Development

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

Build Cytoscape from source code
Develop simple and complex plugins in Java
Rich Cytoscape Application Programming Interface (API)
Active developer community
Write simple functions with scripting languages, including Ruby, Python, Groovy, and JavaScript