Eyeo show & tell about Cytoscape

1. Cytoscape
An open-source ecosystem for complex
network analysis and visualization
Kei Ono
kono@ucsd.edu
The Cytoscape Consortium/
UC,San Diego Dept.of Medicine
Bioinformatics Software Engineer

2. Some Images
from Our Recent Projects

3. A gene ontology inferred from molecular networks. Dutkowski J,
Kramer M,Surma MA,Balakrishnan R,Cherry JM,Krogan NJ,Ideker
T., Nature Biotechnology 2013 Jan;31(1):38-45.
NeXO Web: the NeXO ontology database and visualization
platform. Dutkowski J, Ono K,Kramer M, Yu M, Pratt D,Demchak B,
Ideker T., Nucleic Acids Res. 2014 Jan;42(Database issue).

4. Using deep learning to model the hierarchical structure and function of a cell.
Ma J,Yu MK,Fong S,Ono K,Sage E,Demchak B,Sharan R,Ideker T. Nat Methods. 2018 Mar 5. doi: 10.1038/
nmeth.4627.PMID: 29505029

5. HiView:
Universal browser for
hierarchical data

6. Today’s Topic:
Network Visualization Tool
for everyone

7. Network?

8. Networks appear everywhere…
Internet
Social networks
Protein/gene interactions

9. Tokyo Railway
As a network diagram

10. Citation Network
From Pubmed ID 16904174
a.k.a. Yamanaka Paper

11. Network Data?

12. https://github.com/melaniewalsh/sample-social-network-datasets
Typical network data file
( Edge List )

13. ????

15. Podrick Varys
Joffrey
Orell
Cressen
Gilly
SalladhorCraster
Rattleshirt
Styr
Ygritte
Karl
Lothar
Rickon
Rickard
BranHodor
Nan
Roose
Brynden
Ramsay
Tyrion
Brienne
Cersei
Tywin
Edmure
Catelyn
Petyr
Lysa
Sansa Renly
Anguy
Jojen
Meera
Samwell
Luwin
Theon
Eddison
Alliser
Grenn
Melisandre
Dalla
Bowen
ManceQhorin
Walder
LorasMarillion
Jeyne
StannisRobert
Thoros
Janos
Beric
Jon
Eddard
Aemon
Gendry
Val
Balon
Sandor
Hoster
Jaime
Arya
Robb
Belwas
Kraznys
Drogo
Irri
Daenerys
Aegon
Daario
Jorah
Illyrio
Worm
Missandei
Ellaria
Rakharo
Oberyn
Bronn
Viserys
Rhaegar
Elia
Barristan
ShireenDavos
Qyburn
Jon Arryn
Aerys
Meryn
Pycelle
Ilyn
Gregor
Walton

16. DrogoDaenerys JorahKraznys
Daario
Irri
Aegon
Missandei
Rakharo
BarristanRhaegar
Worm
Belwas
Viserys
Robert

17. Cytoscape
An open-source ecosystem for complex
network analysis and visualization

19. 2003

20. No Gmail
No Google Maps
2003:
Before-Web App Era
(from wikipedia)

21. 2003:
Cytoscape v1
A Java Desktop Application

22. 2019: Cytoscape v3.7.1

23. Cytoscape !=
Desktop Application

24. Cytoscape = Ecosystem
= Collection of applications and libraries
for network analysis and visualization

25. REST API Support
• Language-agnostic
• Enable users to automate
their workflows
• Works nicely with other
popular tools:
• igraph
• NetworkX
• Graphviz
• graph-tool
https://cytoscape.org/cytoscape-tutorials/presentations/advanced-automation-2018-sib.html#/

27. CyJupyter:
Cytoscape.js widget for
Jupyter Notebook

28. CyJupyterLab:
Cytoscape.js extension for
JupyterLab

29. Summary:

30. Cytoscape =
Domain-Independent
(Not only for biologists!)

31. Cytoscape = Ecosystem
Desktop w/ REST API Support
JavaScript Library for Web Developers
Jupyter Notebook / Lab Extension for Data Scientists

32. Cytoscape project
is still very active!

33. Thank you!
Cytoscape
https://cytoscape.org/
Cytoscape.js
http://js.cytoscape.org/
Keiichiro Ono - kono@ucsd.edu
Twitter: @c_z
* All network images in this slide deck are created with Cytoscape