Cytoscape is an

open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

software platform A computing platform or digital platform is an environment in which a piece of software is executed. It may be the hardware or the operating system (OS), even a web browser and associated application programming interfaces, or other underlying ...

for visualizing molecular interaction networks and integrating with

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The ...

profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...

software architecture by anyone and plugin community development is encouraged. Cytoscape also has a

JavaScript JavaScript (), often abbreviated as JS, is a programming language that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of Website, websites use JavaScript on the Client (computing), client side ...

-centric sister project name
Cytoscape.js
that can be used to analyse and visualise graphs in JavaScript environments, like a browser.

History

Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002, and v1.0 was released in March 2003. Version 1.1.1 is the last stable release for the 1.0 series. Version 2.0 was initially released in 2004; Cytoscape 2.83, the final 2.xx version, was released in May 2012. Version 3.0 was released Feb 1, 2013, and the latest version, 3.4.0, was released in May 2016.

Development

The Cytoscape core developer team continues to work on this project and released Cytoscape 3.0 in 2013. This represented a major change in the Cytoscape architecture; it is a more modularized, expandable and maintainable version of the software.
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Usage

While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage. Cytoscape can visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). A vital aspect of the software architecture of Cytoscape is the use of plugins for specialized features. Plugins are developed by core developers and the greater user community.

Features

Input * Input and construct molecular interaction networks from raw interaction files (SIF format) containing lists of protein-protein and/or protein–DNA interaction pairs. For yeast and other model organisms, large sources of pairwise interactions are available through the BIND and

TRANSFAC TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription facto ...

databases. User-defined interaction types are also supported. * Load and save previously-constructed interaction networks in GML format (Graph Modelling Language). * Load and save networks and node/edge attributes in an XML document format called

XGMML XGMML (the eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. Technically, while GML is not related to XML nor SGML, XGMML is an XML application that is so designed that there's ...

(eXtensible Graph Markup and Modeling Language). * Input mRNA expression profiles from tab- or space-delimited text files. * Load and save arbitrary attributes on nodes and edges. For example, input a set of custom annotation terms for your proteins, create a set of confidence values for your protein–protein interactions. * Import gene functional annotations from the

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...

(GO) and

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...

databases. * Directly import GO terms and annotations from OBO and Gene Association files. * Load and save state of the cytoscape session in a cytoscape session (.cys) file. Cytoscape session file includes networks, attributes (for node/edge/network), desktop states (selected/hidden nodes and edges, window sizes), properties, and visual styles. Visualization * Customize network data display using powerful visual styles. * View a superposition of gene expression ratios and p-values on the network. Expression data can be mapped to node color, label, border thickness, or border color, etc. according to user-configurable colors and visualization schemes. * Layout networks in two dimensions. A variety of layout algorithms are available, including cyclic and spring-embedded layouts. * Zoom in/out and pan for browsing the network. * Use the network manager to easily organize multiple networks. And this structure can be saved in a session file. * Use the bird's eye view to easily navigate large networks. * Easily navigate large networks (100,000+ nodes and edges) by an efficient rendering engine. Analysis * Plugins are available for network and molecular profile analysis. For example: ** Filter the network to select subsets of nodes and/or interactions based on the current data. For instance, users may select nodes involved in a threshold number of interactions, nodes that share a particular GO annotation, or nodes whose gene expression levels change significantly in one or more conditions according to p-values loaded with the gene expression data. ** Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of interactions, i.e. interaction subnetworks, whose genes show particularly high levels of differential expression. The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes. ** Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein–protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.

References

External links