Cytoscape.js: a graph theory library for visualisation and analysis

By Max Franz, C. Lopes, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader. Bioinform., 2015

661 citations recorded by the source corpus.

Summary: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Availability and implementation: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. Contact: gary.bader@utoronto.ca

Subfields: Molecular Biology, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/b9d26450520aa98e6ccb1b2e11a48fec29f273b9

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Roded Sharan
2. Trey Ideker
3. Jaak Vilo
4. Mike Tyers
5. Lorrie Boucher
6. Yuxing Liao
7. Zhiao Shi
8. Tambet Arak

In Statistical and Nonlinear Physics

1. Trey Ideker
2. Roded Sharan
3. Quaid D. Morris
4. Bing Zhang
5. Zhiao Shi
6. Jing Wang
7. Jianzhu Ma

Citations in the corpus

• WorldTree V2: A Corpus of Science-Domain Structured Explanations and Inference Patterns supporting Multi-Hop Inference (2020, methodology): “The tool runs in the Chrome web browser, and was implemented in node.js4, with the Cytoscape.js library (Shannon et al., 2003; Franz et al., 2015) used for graph visualization.”
• g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, positive): “js JavaScript library (25) to visualize these networks and provide all interaction data as text.”
• Using deep learning to model the hierarchical structure and function of a cell (2018, methodology): “On the front end, the web interface is built on cytoscape.js 51 and an in-house D3 (ref.”
• WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs (2019, methodology): “We have changed the implementation of the DAG from the obsolete Cytoscape Web library to the Cytoscape.js library (15), removing the need for the Flash plugin.”
• FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations (2020, methodology): “js was used to visualize regulation networks on the web page (11).”
• The BioGRID interaction database: 2017 update (2016, background): “js platform (71) to display interactive graph-based data representations.”
• FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations (2022, methodology): “js was used to visualize pathway and regulation network on the webpage (41).”
• GeneMANIA update 2018 (2018, background): “The app has a new, minimalistic design that focusses on the full-screen, interactive network visualization––which is powered by Cytoscape.js (14).”