Cytoscape.js protocols

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Cytoscape.js specifications

Information


Unique identifier OMICS_10135
Name Cytoscape.js
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Gary Bader <>

Publication for Cytoscape.js

Cytoscape.js in pipeline

2016
PMCID: 5104318
PMID: 27832061
DOI: 10.1371/journal.pcbi.1005128

[…] are useful sources of visualization methods to display all or selected subsets of large, complex, and heterogeneous biological data sets []. for example, jsphylosvg [] draws phylogenetic trees and cytoscape.js [] draws networks. often an artistically talented student can be recruited to help with this, but consider hiring a professional consultant on larger projects., search options […]


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Cytoscape.js in publications

 (15)
PMCID: 5811672
PMID: 29497493
DOI: 10.5256/f1000research.13762.r27544

[…] in different compartments. the objective was to showcase how cellmap can simplify ppi hairballs. we visualize the same ppi network using cellmap ( ) and cytoscape in the form of the cytoscape.js version used by hippie ( ) and the cytoscape desktop version ( )., none of the three viewers solves the ppi hairball problem completely. without zooming in, the information density […]

PMCID: 5765210
PMID: 29270911
DOI: 10.1007/s10522-017-9741-5

[…] using a combination of hypertext markup language (html), cascading style sheets (css), and javascript and has been tested in all major browsers. interactive network visualizations are rendered using cytoscape.js (franz et al. )., to determine if the observed gene-based set overlaps are defined by the sizes of the respective datasets, they were compared to a background distribution. […]

PMCID: 5540468
PMID: 28804499
DOI: 10.1155/2017/1278932

[…] to remain the number-one player for biological network analysis. a network visualized by cytoscape is shown in . cytoscape is available at http://www.cytoscape.org/., finally, cytoscapeweb [] and cytoscape.js are separate projects. they are two very strong efforts aiming to incorporate cytoscape's main visual functionalities in browser-based applications, something that of course […]

PMCID: 5471944
PMID: 28617226
DOI: 10.1186/s12859-017-1642-8

[…] some known functional association to the drug (based on stitch/string database)., to allow an interactive presentation of the evidence networks, a web-portal was created using the javascript library cytoscape.js [] and built into the main eddy-ctrp web-portal (http://biocomputing.tgen.org/software/eddy/ctrp). these evidence networks can be accessed at two places in the portal. first, […]

PMCID: 5831934
PMID: 29657291
DOI: 10.3390/ncrna3020020

[…] that deals with substructures computation has been developed in java, and the functional enrichment procedure has implemented using the r statistical environment []. the web application also employs cytoscape.js [] for displaying subpathways. furthermore, to minimize user waiting time, all the computations are cached to be reused; therefore no user private data are stored. in , we report […]


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Cytoscape.js institution(s)
The Donnelly Centre, University of Toronto, Toronto, ON, Canada
Cytoscape.js funding source(s)
NRNB (U.S. National Institutes of Health, National Center for Research Resources grant P41 GM103504); NIH grants R01GM070743 and U41HG006623

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