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cytoscape / cytoscape.js

Graph theory (network) library for visualisation and analysis
https://js.cytoscape.org
MIT License
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Who uses Cytoscape.js? #914

Open maxkfranz opened 9 years ago

maxkfranz commented 9 years ago

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

Please include:

d47853 commented 6 years ago

GCHQ uses Cytoscape.js in their UI for Gaffer, an open source graph database.

vicscott commented 6 years ago

UESTC http://cefg.uestc.edu.cn/Mslr/index.html

ksebby commented 5 years ago

xD Bio Inc. We use cytoscape to display bioinformatics workflows. Main site truwl.com example: https://truwl.com/workflows/detail/ENCODE%20ATAC-seq%20pipeline

ortega2247 commented 5 years ago

Vanderbilt University We use cytoscapejs at the Lopez lab to generate static and dynamic networks of systems biology models pysbjupyter

Hoogkamer commented 5 years ago

Interactive MetroMap visualisation for process descriptions (DEMO)

image

https://github.com/Hoogkamer/MetroMap

ghamarian commented 5 years ago

We use cytoscapejs to generate tensorflow models graphically. https://www.machine2learn.com/deep-learning-model-generator/

mammmals commented 5 years ago

We use cytoscape.js to display protein-protein interaction data for the genome-scale BioPlex Interactome Project: http://bioplex.hms.harvard.edu/bioplexDisplay/index.php

sepro commented 5 years ago

I used cytoscape.js at my previous job at the Max Planck Institute for Molecular Plant Physiology in CoNekT to visualize co-expression networks like this.

nitinreddy3 commented 5 years ago

We use cytoscape to display different models

Organization name: Intercax Org website: http://intercax.com

wrnrlr commented 5 years ago

We use is as the basis of our graph explorer:

Almanax https://alman.ax/#/about

smith commented 5 years ago

New Relic https://newrelic.com/platform

Used in the New Relic One service map.

scastlara commented 5 years ago

PlanNET https://compgen.bio.ub.edu/PlanNET

Used for displaying protein-protein interactions and genomic data for planarians.

ghost commented 5 years ago

Cytoscape.js is the basis for this visualization of decentralized social networks like Mastodon (the "fediverse"): https://www.fediverse.space

taurenshaman commented 5 years ago

Lore (A note platform)
http://lore.chuci.info

(Mind) Note Examples:
http://lore.chuci.info/taurenshaman/mind/ac6231844c4a4aeaba899f11d14bfa29

http://lore.chuci.info/taurenshaman/mind/67cef0e751944e008d6618ea76af8ecb

http://lore.chuci.info/taurenshaman/mind/fa308b5268c9432c8149737088a2c893

mind-xgzsz-jianghu

josejulio commented 5 years ago

Kiali https://www.kiali.io/

Service mesh observability kiali

fosterfarrell9 commented 5 years ago

We use it to visualize relations between mathematical content in our E-Learning Platform MaMpf https://mampf.mathi.uni-heidelberg.de

math_content

pash90 commented 5 years ago

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 commented 5 years ago

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 commented 4 years ago

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/

jhk0530 commented 4 years ago

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 commented 4 years ago

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

hackertarget commented 4 years ago

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

fcoskunn commented 4 years ago

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 commented 4 years ago

RIFMClusterExample

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

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

geotheory commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

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!

jhk0530 commented 4 years ago

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 commented 4 years ago

Nice work @jhk0530 :)

cjfpainter commented 4 years ago

Organization: Headstarter Ltd., Cork Website: https://www.headstarter.pro

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!

smith commented 4 years ago

The Elastic APM Service Map uses Cytoscape.js.

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

MirzayevFarid commented 4 years ago

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

AdrienSolacroup commented 3 years ago

Hi ! I develop a framework in javascript dedicate to specific thematics (land planning, environment, ecology and resilience). And I use cytoscape for the main visual features.

Organisation name; GREZI Link to organisation site : https://grezi.fr

maxkfranz commented 3 years ago

@AdrienSolacroup, that sounds great. Do you have a Github page or a demo that we could link to? The links on the page don't work for me, and I expected I'd see a project description if I clicked the «découvrir» button.

AdrienSolacroup commented 3 years ago

@maxkfranz Thank you :) I'm currently preparing a launching so the website is clearly incomplete. I can give you a staging adress for a demo. But maybe it's worth it to reference GREZI after I finish the website ?

yogeshkodei commented 3 years ago

Organization name: Tripudio Technologies We develop UI as a service using Cytoscape.

tolunayakbulut commented 3 years ago

Hi, Organisation name: Global CTO Forum Link to organisation site: https://globalctoforum.org/

blazespinnaker commented 3 years ago

We are using it to build an OS VPL platform for python, similar to jupyter but visual. Github repo will be forthcoming. If it isn't too off topic, I'd like take a second to applaud the Cytoscape org and in particular Max for his fantastic stewardship of this very important OS framework.

maxkfranz commented 3 years ago

We are using it to build an OS VPL platform for python, similar to jupyter but visual. Github repo will be forthcoming. If it isn't too off topic, I'd like take a second to applaud the Cytoscape org and in particular Max for his fantastic stewardship of this very important OS framework.

That's interesting. I'll add the entry once you've posted the link. Thanks

pbylina commented 3 years ago

Hi,

we use cytoscape.js to visualize tests flow in our end-to-end web testing tool. Link do website https://bugbug.io

image

Thanks for your job! We appreciate it very much!

AdrienSolacroup commented 3 years ago

@AdrienSolacroup, that sounds great. Do you have a Github page or a demo that we could link to? The links on the page don't work for me, and I expected I'd see a project description if I clicked the «découvrir» button.

@maxkfranz The website is now online :) : https://grezi.fr/

An here a direct link to the app : https://app.grezi.fr/

manishpatelUK commented 3 years ago

We use this in our machine learning dashboard Organisation: Jiva.ai (www.jiva.ai)

nileshtrivedi commented 3 years ago

We use this at https://LearnAwesome.org for mapping the topic taxonomy for internal usage, and soon might start using it with users too.

steampixel commented 3 years ago

Wanderer.ai uses cytoscape.js for a context graph driven open source chatbot builder: https://wanderer.ai/builder/

Abhi5h3k commented 3 years ago

graphml viwere

UI example

👉 Graphml visualiser 👉 Demo link @ github

ugurdogrusoz commented 3 years ago

https://www.cbioportal.org/

marieBvr commented 3 years ago

AraQTL version 2 (from Wageningen University and Research (WUR, NL) and INRAe (France) https://www.bioinformatics.nl/AraQTL/

HEmile commented 3 years ago

Used in the Juggl plugin for https://obsidian.md Organisation: Juggl https://juggl.io

drawing
Phally commented 3 years ago

We use Cytoscape.js in various data and network related projects at major Dutch telco KPN.

KPN https://www.kpn.com/

Phenomenal project Cytoscape, great job!

cloudronin commented 3 years ago

We use Cytoscape.js for visualizing our Biomedical knowledge graph that is used in Drug Discovery research

Wisecube AI https://www.wisecube.ai/orpheus/

Keep up the good work !!