Cytoscape: Difference between revisions

	Cytoscape home page
Original author(s)	Institute for Systems Biology
Developer(s)	Cytoscape Team
Initial release	July 2002
Stable release	3.8.2 / 29 October 2020; 4 years ago
Written in	Java
Operating system	Any (Java-based)
Type	Image processing
License	LGPL
Website	www.cytoscape.org

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Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression 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 software architecture by anyone and plugin community development is encouraged.^[2]^[3] Cytoscape also has a JavaScript-centric sister project named 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.^[4]

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.

References

^ "Cytoscape 3.8.2 is released!". groups.google.com. Retrieved 11 March 2021.
^ Shannon P, Markiel A, Ozier O, et al. (2003). "Cytoscape: a software environment for integrated models of biomolecular interaction networks". Genome Res. 13 (11): 2498–504. doi:10.1101/gr.1239303. PMC 403769. PMID 14597658.
^ Bell GW, Lewitter F (2006). "Visualizing Networks". DNA Microarrays, Part B: Databases and Statistics. Meth. Enzymol. Vol. 411. pp. 408–21. doi:10.1016/S0076-6879(06)11022-8. ISBN 978-0-12-182816-5. PMID 16939803.
^ Cytoscape Product Roadmap

External links

[Releases-1] "Cytoscape 3.8.2 is released!". groups.google.com. Retrieved 11 March 2021.

[2] Shannon P, Markiel A, Ozier O, et al. (2003). "Cytoscape: a software environment for integrated models of biomolecular interaction networks". Genome Res. 13 (11): 2498–504. doi:10.1101/gr.1239303. PMC 403769. PMID 14597658.

[3] Bell GW, Lewitter F (2006). "Visualizing Networks". DNA Microarrays, Part B: Databases and Statistics. Meth. Enzymol. Vol. 411. pp. 408–21. doi:10.1016/S0076-6879(06)11022-8. ISBN 978-0-12-182816-5. PMID 16939803.

[4] Cytoscape Product Roadmap

[1]

[2]

[3]

[4]

@@ Line 4: / Line 4: @@
 | logo                   = <!-- [[File: ]] -->
 | logo caption           =
-| screenshot             = [[File:CytoscapeHome.png|200px]]
+| screenshot             = CytoscapeHome.png
+| screenshot size        = 200px
 | caption                = Cytoscape home page
 | collapsible            =
-| author                 = [http://www.systemsbiology.org/ Institute of Systems Biology]
+| author                 = [http://www.systemsbiology.org/ Institute for Systems Biology]
-| developer              =
+| developer              = [https://cytoscape.org/development_team.html Cytoscape Team]
 | released               = July 2002<!-- {{Start date|YYYY|MM|DD|df=yes/no}} -->
 | discontinued           =
-| latest release version = 3.2.1
+| latest release version = 3.8.2
-| latest release date    = {{Start date and age|2015|02|11|df=yes/no}}
+| latest release date    = {{Start date and age|2020|10|29|df=yes/no}}<ref name="Releases">
+{{cite web
+|url=https://groups.google.com/g/cytoscape-announce/c/WQas4dkhsZs
+|title=Cytoscape 3.8.2 is released!
+|website=groups.google.com
+|access-date=11 March 2021
+}}</ref>
 | latest preview version =
 | latest preview date    = <!-- {{Start date and age|YYYY|MM|DD|df=yes/no}} -->
-| frequently updated     = <!-- DO NOT include this parameter unless you know what it does -->
 | status                 =
 | programming language   = [[Java platform|Java]]
@@ Line 31: / Line 37: @@
 | AsOf                   =
 }}
-'''Cytoscape''' is an [[open source]] [[bioinformatics]] software platform for [[Visualization (graphic)|visualizing]] [[Metabolic network modelling|molecular interaction networks]] and integrating with [[gene expression]] 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 (programming language)|Java]] software architecture by anyone and plugin  community development is encouraged.<ref>{{cite journal |author=Shannon P, Markiel A, Ozier O |title=Cytoscape: a software environment for integrated models of biomolecular interaction networks |journal=Genome Res. |volume=13 |issue=11 |pages=2498–504 |year=2003 |pmid=14597658 |doi=10.1101/gr.1239303 |url=http://www.genome.org/cgi/content/full/13/11/2498 |pmc=403769|display-authors=etal}}
+'''Cytoscape''' is an [[Open-source software|open source]] [[bioinformatics]] [[software platform]] for [[Visualization (graphic)|visualizing]] [[Metabolic network modelling|molecular interaction networks]] and integrating with [[gene expression]] profiles and other state data. Additional features are available as [[plug-in (computing)|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 (programming language)|Java]] software architecture by anyone and plugin  community development is encouraged.<ref>{{cite journal |vauthors=Shannon P, Markiel A, Ozier O |title=Cytoscape: a software environment for integrated models of biomolecular interaction networks |journal=Genome Res. |volume=13 |issue=11 |pages=2498–504 |year=2003 |pmid=14597658 |doi=10.1101/gr.1239303 |url=http://www.genome.org/cgi/content/full/13/11/2498 |pmc=403769|display-authors=etal}}
-</ref><ref>{{cite journal |author=Bell GW, Lewitter F |title=Visualizing networks |journal=Meth. Enzymol. |volume=411 |issue= |pages=408–21 |year=2006 |pmid=16939803 |doi=10.1016/S0076-6879(06)11022-8}}</ref>  Cytoscape also has a [[JavaScript]]-centric sister project named [http://js.cytoscape.org Cytoscape.js] that can be used to analyse and visualise graphs in JavaScript environments, like a browser.
+</ref><ref>{{cite book |vauthors=Bell GW, Lewitter F |chapter=Visualizing Networks |title=DNA Microarrays, Part B: Databases and Statistics |series=Meth. Enzymol. |volume=411 |pages=408–21 |year=2006 |pmid=16939803 |doi=10.1016/S0076-6879(06)11022-8|isbn=978-0-12-182816-5 }}</ref>  Cytoscape also has a [[JavaScript]]-centric sister project named [http://js.cytoscape.org 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. 1st, 2013, and the latest version, 3.2.0, was released in October 2014.
+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.<ref>[http://cytoscape.wodaklab.org/wiki/Cytoscape_3/ developer's wiki page].</ref> As of February 2015, work is beginning on version 3.3.
+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.<ref>[https://cytoscape.org/roadmap.html Cytoscape Product Roadmap]</ref>
 == Usage ==
-[[Image:Cytoscape network visualization1.png|thumb|450px|Yeast Protein–protein/Protein–DNA interaction network visualized by Cytoscape. Node degree is mapped to node size]]
+[[Image:Cytoscape network visualization1.png|thumb|upright=1.2|Yeast Protein–protein/Protein–DNA interaction network visualized by Cytoscape. Node degree is mapped to node size]]
-While Cytoscape is most commonly used for biological research applications, it is agnostic in terms of usage.  Cytoscape can be used to visualize and analyze network graphs of any kind involving nodes and edges (e.g., social networks). A key 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.
+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]] databases. User-defined interaction types are also supported.
-* Load and save previously-constructed interaction networks in [[Graph Modelling Language|GML]] format (Graph Modelling Language).
-* Load and save networks and node/edge attributes in an XML document format called [[XGMML]] (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]] (GO) and [[KEGG]] 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 [[Force-based algorithms (graph drawing)|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 efficient rendering engine.
-'''Analysis'''
-* Plugins 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.
 == See also ==
 * [[Computational genomics]]
+* [[Graph drawing]]
+* [[JavaScript framework]]
+* [[JavaScript library]]
 * [[Metabolic network modelling]]
 * [[Protein–protein interaction prediction]]
@@ Line 81: / Line 64: @@
 == External links ==
 * {{Official website|http://www.cytoscape.org/}}
-* [http://www.cytoscape.org/cgi-bin/moin.cgi/ Cytoscape wiki]
+** https://cytoscape.org/screenshots.html
+* [http://wiki.cytoscape.org/ Cytoscape wiki]
+* [https://omictools.com/cytoscape-tool Cytoscape omictools webpage]
 {{genomics-footer}}
+{{Graph Analysis Software}}
 [[Category:Bioinformatics software]]

v t e Genomics
Fields	Cognitive genomics Computational genomics Comparative genomics Functional genomics Genome project Human Genome Project Metagenomics Human Microbiome Project Pangenomics Personal genomics Population genomics Sociogenomics Structural genomics
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Structural biology	Proteomics Human proteome project Call-map proteomics Structure-based drug design Expression proteomics
Research tools	2-D electrophoresis Mass spectrometer Electrospray ionization Matrix-assisted laser desorption ionization Matrix-assisted laser desorption ionization-time of flight mass spectrometer Microfluidic-based tools Isotope affinity tags Chromosome conformation capture
Organizations	DNA Data Bank of Japan (JP) European Molecular Biology Laboratory (EU) National Institutes of Health (USA) Wellcome Sanger Institute (UK)
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v t e Graph analysis software
Free	Cytoscape Graphviz Gephi igraph Microsoft Automatic Graph Layout NetworkX Tulip
Proprietary	Maple Mathematica