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Who uses Cytoscape.js? #914

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maxkfranz opened this issue Apr 24, 2015 · 82 comments
Open

Who uses Cytoscape.js? #914

maxkfranz opened this issue Apr 24, 2015 · 82 comments
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@maxkfranz
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@maxkfranz maxkfranz commented Apr 24, 2015

It would be nice to include a list of organisations that use Cytoscape.js in the docs.

Please include:

  • Organisation name
  • Link to organisation site
@danieljue
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@danieljue danieljue commented Apr 28, 2015

@maxkfranz
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@maxkfranz maxkfranz commented Apr 28, 2015

@maxkfranz
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@maxkfranz maxkfranz commented Apr 28, 2015

@maxkfranz
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@maxkfranz maxkfranz commented Apr 28, 2015

Later:

GeneMANIA
http://genemania.org

@keiono
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@keiono keiono commented Apr 28, 2015

Also, we are using it:

CyNetShare

http://cynetshare.ucsd.edu/

@ktei
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@ktei ktei commented May 10, 2015

@robmosca
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@robmosca robmosca commented May 12, 2015

@EDreven
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@EDreven EDreven commented Jun 4, 2015

video instruction.
http://www.kartoteka.ru/vizual
The module itself is not free.

@keiono
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@keiono keiono commented Jun 4, 2015

It's still in beta, but our embedded Jupyter (IPython) Notebook widget uses cytoscape.js:

https://github.com/idekerlab/py2cytoscape

@maxkfranz
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@maxkfranz maxkfranz commented Dec 11, 2015

@maxruby
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@maxruby maxruby commented Dec 12, 2015

Visual Interaction GmbH: http://www.mygaze.com

@patbuergin
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@patbuergin patbuergin commented Jan 9, 2016

GIGRAPH – Network Visualization for Excel
https://gigraph.io
(non-commercial, private project)

@mabossert
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@mabossert mabossert commented Jan 19, 2016

I use at Cray inc. as part of a front-end analytics application run on our supercomputers.
http://www.cray.com

@danmaclean
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@danmaclean danmaclean commented Jan 26, 2016

PINet - http://pinet.tsl.ac.uk
Tool for The Sainsbury Laboratory network analyses

@YMA-MDL
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@YMA-MDL YMA-MDL commented Feb 12, 2016

Ganister - http://www.ganister.eu/
Configuration management solution for Electronic/HighTech/Defense&Security companies

maxkfranz added a commit that referenced this issue Feb 25, 2016
@AoDev
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@AoDev AoDev commented Mar 19, 2016

Trace: https://trace.risingstack.com/

Microservices Visualized
Anomaly detection, distributed transaction tracking and process monitoring for your services.

@michalhabala
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@michalhabala michalhabala commented Apr 7, 2016

Graphlytic - Graph BI platform
http://graphlytic.sk/

@jfreyreg
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@jfreyreg jfreyreg commented Apr 25, 2016

Abasy Atlas: A comprehensive atlas of systems, global network properties, and system-level elements shaping regulatory networks across bacteria
http://abasy.ccg.unam.mx

@narseo
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@narseo narseo commented Jun 8, 2016

ICSI Haystack Project to show tracking activity on mobile apps:

https://haystack.mobi/panopticon/

@Malalama
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@Malalama Malalama commented Jun 9, 2016

A friend and I have been working on Musicalized, a Family Tree of All Music Genres:

http://en.musicalized.com/full

Happy to receive some feedback!

@maxkfranz maxkfranz self-assigned this Jun 10, 2016
@maxkfranz maxkfranz added the pinned label Oct 1, 2019
@pash90
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@pash90 pash90 commented Oct 2, 2019

My company uses Cytoscape to display the graph of a user's chatbot. Different pathways possible and elements of each pathway.

Organisation: Stackchat
Link: https://stackchat.com

@smpaley
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@smpaley smpaley commented Oct 2, 2019

SRI International, Bioinformatics Research Group uses it for the Pathway Collages (https://biocyc.org/pathway-collage-info) tool that is part of the BioCyc.org website.

pwycollage

@jelmerjellema
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@jelmerjellema jelmerjellema commented Oct 7, 2019

Spin in het Web b.v. (www.spininhetweb.nl) for University of Amsterdam: we use cytoscape to let students create conceptual models for qualitative simulation, and to show the simulation results. https://dynalearn.nl/

maxkfranz added a commit that referenced this issue Oct 7, 2019
maxkfranz added a commit that referenced this issue Oct 7, 2019
@jhk0530
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@jhk0530 jhk0530 commented Oct 15, 2019

Hi, we built R/Shiny Appication "GScluster" using Old version of cytoscape.js ( ver 2.4.1 ) for network-weighted gene-set clustering and network visualization few month ago.

GScluster https://github.com/unistbig/GScluster

also we built R Package "shinyCyJS" that connects cytoscape.js and R/shiny with recent version of cytoscape.js. ( ver 3.4.2 )

shinyCyJS https://github.com/unistbig/shinyCyJS

now we are working with shinyCyJS to replace older version of GScluster's cytoscape.js

p.s.)
we tried to use RCyjs http://www.bioconductor.org/packages/release/bioc/html/RCyjs.html
but it didn't supports to shiny application.

here's our group

UNIST Bioinformatics Group. https://sites.google.com/site/bigunist2/

@IfatChitin
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@IfatChitin IfatChitin commented Oct 28, 2019

Panaya uses cytoscape to visualize relations.
For example relations between Salesforce components in Panaya ForeSight:

image
We use breadthfirst layout in order to get a layered layout, then we order the nodes further more (in the first level we place the most connected nodes in the center, in all other layers we place each child as close as possible to its parent.)
image
We love working with cytoscape, with its awesome and rich API, great performance and fast solutions and releases.
Thank you!

Panaya: https://www.panaya.com
Panaya ForeSight: https://www.panaya.com/product/salesforce-foresight

maxkfranz added a commit that referenced this issue Nov 4, 2019
@ghost
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@ghost ghost commented Nov 4, 2019

https://hackertarget.com/ uses Cytoscape to visualise an organisations attack surface. Mapping relationships between DNS records, ASN's and Internet infrastructure for an organisation.

It is an excellent library for visualising large numbers of nodes.

image

maxkfranz added a commit that referenced this issue Nov 19, 2019
maxkfranz added a commit that referenced this issue Nov 19, 2019
@fcoskunn
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@fcoskunn fcoskunn commented Dec 22, 2019

GLB301 Simulation uses cytoscape in order to demonstrate the infrastructure network and improved version of the infrastructure network with ad-hoc communication. If a node is not inside one of the area of base stations, it looks for the other nodes which have the internet connection. By this improvement, the capacity and range of a base station increases.

We use lots of the features of cytoscape. Thanks a lot!

image

The Github Repository: https://github.com/fcoskunn/Cytoscape-Network-Demo

http://www.agu.edu.tr/

@mngilmore
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@mngilmore mngilmore commented Jan 3, 2020

RIFMClusterExample

Organization: http://www.rifm.org
Website: https://rifmdatabase.rifm.org/rifmweb/

We use cytoscape.js to visualize clustered chemicals. Thank you!

@geotheory
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@geotheory geotheory commented Feb 4, 2020

also we built R Package "shinyCyJS" that connects cytoscape.js and R/shiny with recent version of cytoscape.js. ( ver 3.4.2 )

shinyCyJS https://github.com/unistbig/shinyCyJS

@jhk0530 interested to hear how development is progressing. Do you anticipate documentation anytime soon? I'm wondering what layouts will be supported.

@jhk0530
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@jhk0530 jhk0530 commented Feb 4, 2020

@geotheory Hi, thank you for your interest. currently, shinyCyJS supports for 5 layout. klay, fcose, spread, dagre, cola. I'm not sure about time will be either soon or not, but I'll try to document as possible. If you have more questions, mail me. Again thanks.

@binDongKim
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@binDongKim binDongKim commented Feb 24, 2020

Organization: Naver Pinpoint
Website: https://naver.github.io/pinpoint/

Pinpoint is a leading open-source APM and currently using this awesome library on displaying the server-map. Many thanks!

maxkfranz added a commit that referenced this issue Mar 16, 2020
maxkfranz added a commit that referenced this issue Mar 16, 2020
@jhk0530
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@jhk0530 jhk0530 commented Mar 27, 2020

Site : https://github.com/jhk0530/shinyCyJS

@geotheory

I deployed R package shinyCyJS to CRAN.
Which supports basic features of cytoscape.js for Shiny framework of R language.

Bests,

@geotheory
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@geotheory geotheory commented Mar 31, 2020

Nice work @jhk0530 :)

@cjfpainter
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@cjfpainter cjfpainter commented May 25, 2020

Organization: CJFP & Associates
Website: https://sherlock.scalingo.io

We use extended collocation analysis to expose salient features in text, and we use Cytoscape.js to expose those features as an interactive map that can be used to filter the text.

For example, Covid researchers can keep up to date with Springer Nature journals by mapping the abstracts into an index which they can then use to find common features in context.

In the image below abstracts are filtered by the selected edge in the map between "Respiratory" and "Syndrome", with the matches highlighted in the text below.

image

The website also features demonstrations for Wikipedia pages, and PDF files that you upload to the browser only. Enjoy!

maxkfranz added a commit that referenced this issue Jun 10, 2020
maxkfranz added a commit that referenced this issue Jun 10, 2020
@smith
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@smith smith commented Aug 25, 2020

The Elastic APM Service Map uses Cytoscape.js.

Organisation name: Elastic
Link to organisation site: https://www.elastic.co/

@MirzayevFarid
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@MirzayevFarid MirzayevFarid commented Sep 1, 2020

Organisation name: Radity
Link to organisation site: https://radity.com

maxkfranz added a commit that referenced this issue Sep 14, 2020
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