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Cytoscape.js specifications


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


No version available


  • person_outline Gary Bader

Publication for Cytoscape.js

Cytoscape.js citations


IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics

Sci Rep
PMCID: 5847565
PMID: 29531263
DOI: 10.1038/s41598-018-22631-z

[…] e result of user queries for these associations in two ways: (a) A table of associations with references to literature sources, and (b) A network visualization of the associations which is powered by Cytoscape.js (Fig. ). In addition, users can also download the result of their queries for different associations of medicinal plants as a tab-separated list using the available export option in the w […]


iPTMnet: an integrated resource for protein post translational modification network discovery

Nucleic Acids Res
PMCID: 5753337
PMID: 29145615
DOI: 10.1093/nar/gkx1104
call_split See protocol

[…] erlying system components to support interactive scientific queries and visualization of PTM data. The website provides two types of visualization: the Cytoscape () network view, implemented with the Cytoscape.js (version 2.4.2) graph theory library, and the multiple sequence alignment view. Multiple sequence alignments are performed using MUSCLE (). […]


NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium scale biological networks

BMC Res Notes
PMCID: 5513407
PMID: 28705239
DOI: 10.1186/s13104-017-2607-8

[…] e of igraph-R library [] and plots are generated through R and plotly []. Static network visualizations are offered by the d3 library whereas dynamic network visualization is provided by CytoscapeWeb/Cytoscape.js [, ]. […]


Contextualization of drug mediator relations using evidence networks

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

[…] the interpretability of the EDDY-CTRP results by generating evidence networks of the most relevant intermediate genes using the STRING and STITCH knowledge-bases. With these evidence networks and our Cytoscape.js-based user interface, we expect that the EDDY-CTRP results can be used to form hypotheses based on these contextualized drug-mediator pairs.Besides facilitating drug-mediator pair interpr […]


CorNet: Assigning function to networks of co evolving residues by automated literature mining

PLoS One
PMCID: 5436653
PMID: 28545124
DOI: 10.1371/journal.pone.0176427
call_split See protocol

[…] The CMA network visualization tool was built using cytoscape.js (a JavaScript graph visualization library)[] and jquery (user interface libraries). In this HTML based network viewer nodes represent alignment positions (with the MSA position number ind […]


SBSPKSv2: structure based sequence analysis of polyketide synthases and non ribosomal peptide synthetases

Nucleic Acids Res
PMCID: 5570206
PMID: 28460065
DOI: 10.1093/nar/gkx344
call_split See protocol

[…] enzymes involved in the characterized PKs/NRPs pathway have been stored. The PK and NRP pathways have been represented as interactive graphs (Figure ). The pathway pages use embedded JavaScript-based Cytoscape.js (). Each graph starts with the starter moiety and catalogs the intermediate steps to terminate at the complete metabolite. The nodes of the graph represent the biosynthetic intermediates […]


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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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