Cytoscape is an open-source platform for biological network data integration, analysis, and visualization, recently updated to version 3.4 with new features such as a network view manager, app collections, and performance improvements. The platform supports web applications via Cytoscape.js, which allows users to share and visualize network data interactively. The document discusses enhancements aimed at improving user experience and acknowledges the importance of a strong community for continuous development and support.

1. What’s New In Cytoscape?
Keiichiro Ono
UCSD Trey Ideker Lab
Cytoscape Core Team
SDCSB Workshop
5/19/2016@Sanford

2. Keiichiro Ono
Cytoscape Core Developer
since 2005
@UCSD Trey Ideker Lab
Area of Interest:
Biological Data Integration &
Visualization

3. Outline
- Cytoscape Project Updates
- Cytoscape Core
- Cytoscape and the Web
- Cytoscape Ecosystem and CI

4. Quick Introduction to
Cytoscape

5. What is Cytoscape?

6. An Open Source Platform for Biological Network Data
Integration, Analysis and Visualization
Cytoscape

7. Cytoscape 3.4

8. Cytoscape
- Open Source: LGPL
- Free for both commercial and academic use
- Developed and maintained by universities, companies, and research
institutions
- De-facto standard software in biological network
research community
- 13k downloads / month
- Expandable by Apps
- Platform, not a stand-alone desktop application

9. C. Elegans Interactome from BioGRID Database
?

10. Biological Networks
- Tell us anything by themselves
- Just a big hairball…

11. Module 1
Need a tool to extract
meaningful biological modules

13. Basic Workflow

14. Networks
Public Interaction Databases

15. List of
Genes

16. Other Data

19. APPS.CYTOSCAPE.ORG

20. Real World
Use Cases
cytoscape-publications.tumblr.com

21. Cytoscape Ecosystem

22. Cytoscape
For Desktop Cytoscape 3.4
Publish to the web
For Building Web Applications Cytoscape.js
Interaction Data
Repository
NDEx
Cyberinfrastructure (CI)
Sample Services
Fast ID Mapping
Network Image Generator
Format converter
Data Format CX
Job Router ELSA
Visualization Widgets
Network Widget
Table Widget
Composite Widget NDEx Valet

23. For Desktop Cytoscape 3.4
For Building Web Applications Cytoscape
Interaction Data
Repository

24. Cytoscape 3.4

25. Cytoscape 3.4
• Latest version of Cytoscape
Desktop application
• New Features:
• New Network View Manager
• App Collections
• Performance Improvements for
browsing large number of
networks (grid view)
• Lots of bug fixes

26. New Network View Manager

27. Grid View

28. Grid View
• Display all networks as
tiles of network images
• Can easily handle
hundreds of networks
without any
performance penalty

29. Detached View

30. Detached View
• Display networks in
separate windows
• Useful when you have
large workspace (e.g.
dual display)

31. App Collections

32. App Collections
• Users can install multiple
Apps at once
• Organized for specific use
cases
• Mass Spec
• Omics Analysis
• Functional Enrichment
• EmrichmentMap

33. Cytoscape 3.4.0
www.cytoscape.org/download.php
Download Link:

34. Cytoscape
For Desktop Cytoscape 3.4
Publish to the web
For Building Web Applications Cytoscape.js
Interaction Data
Repository
NDEx
Cyberinfrastructure (CI)
Sample Services
Fast ID Mapping
Network Image Generator
Format converter
Data Format CX
Job Router ELSA
Visualization Widgets
Network Widget
Table Widget
Composite Widget NDEx Valet

35. 3.4
Publish to the web
ons Cytoscape.js
n Data
ry
NDEx

36. Cytoscape and The Web

37. 11 Years Ago…

39. 2005
- Cytoscape 2.2: a Java Desktop Application
- Google released an application called
Google Maps beta
- “Re-discovery” of JavaScript, or Ajax
- Virtually no smartphone market

40. Today

42. Today
- JavaScript is a programming language for
large-scale applications
- Tablets and other touch-based devices are
important platform for data visualization
- Web is a competitive application platform

43. Our Approach to the Web
- Cytoscape project should support use cases such as:
- Sharing network data over the web
- Visualizing network data on web browsers

44. cytoscape.js

45. - A JavaScript Library
- NOT A WEB APPLICATION!
- A building block for web apps
- For web application programmers
- But there are many web applications using
Cytoscape.js
cytoscape.js

46. http://bit.ly/1W4vBzk

47. bit.ly/22hkOlv

48. cytoscape.js
- Fast enough for relatively
large networks
- Stable
- Open source (MIT)

49. ScienceDirect App
Publish your networks as interactive diagrams
Interactive paper figures
Collaboration Project with Elsevier

50. Network Diagrams in Papers
- Problem:
- OK for small networks/pathways
- Does not helpful for large
networks
- Solution:
- Make them interactive
- Pan / Zoom

51. https://www.elsevier.com/books-and-journals/content-innovation/interactive-network-viewer

56. Example:
Host cell interactome of PA protein of H5N1 influenza
A virus in chicken cells – Journal of Proteomics
http://www.sciencedirect.com/science/article/pii/S1874391916300215

57. How to Export your Networks
for Interactive Viewers

60. Preview

63. Demo
Load a Network
Preview in Web Browser
Export

64. cynetshare
A web application using cytoscape.js

67. bit.ly/1DNmetV

68. bit.ly/1DNmetV
- Location of Network File
- Visual Style
- Zoom Level
- Viewable Area

69. Cytoscape
For Desktop Cytoscape 3.4
Publish to the web
For Building Web Applications Cytoscape.js
Interaction Data
Repository
NDEx
Cyberinfrastructure (CI)
Sample Services
Fast ID Mapping
Network Image Generator
Format converter
Data Format CX
Job Router ELSA
Visualization Widgets
Network Widget
Table Widget
Composite Widget NDEx Valet

70. P
For Building Web Applications Cytoscape.js
Interaction Data
Repository
NDEx
Sample Services
Fast ID Mapping
Network Image Generator
Format converter

71. e
Interaction Data
Repository
NDEx
Cyberinfrastructure (CI)
Sample Services
Fast ID Mapping
Network Image Generator
Format converter
Data Format CX
Job Router ELSA
Visualization Widgets
Network Widget
Table Widget
Composite Widget NDEx Valet

72. Cytoscape Cyberinfrastructure

73. Cyberinfrastructure?

74. –Wikipedia
Cyberinfrastructure:
Research environments that support advanced
data acquisition, data storage, data management,
data integration, data mining, data visualization
and other computing and information processing
services distributed over the Internet beyond the
scope of a single institution

75. ?

76. Computing
Infrastructure
Community

77. Computing Infrastructure

78. Problems in Bioinformatics
- No more free lunch
- Even if you buy expensive machines, you cannot get
free performance gain anymore. You have to design
your code for massively distributed environment.
(From Scale-up to Scale-out)
- This is a problem especially when you analyze
omics-scale data sets

79. Problems in Bioinformatics
- Complex Data Analysis Pipeline
- Need to build pipeline by connecting multiple
resources, or services
- Needs for complex, customized data visualization

80. Problems in Bioinformatics
- Reproducibility
➡ Building, deploying, and maintaining reproducible
data analysis / visualization pipeline is not straight-
forward

81. Data
Preparation
Analysis Visualization

82. ALL tools should work nicely together with other
popular software packages

83. REST

84. What is cyREST?
- Platform-independent, RESTful API module for Cytoscape
- Means you can access basic Cytoscape data objects
programmatically
- Now this is a Cytoscape Core feature!
REST

85. Two sides of modern biology
✔

86. Use Cases
- I have 200 networks in my session and I need to create
one PDF per view. How can I do it with Cytoscape?
- I need to use igraph for network analysis, but its
visualization feature is limited. I want to use Cytoscape
as an external visualization engine for R.
- Usually I use IPython Notebook to record my work.
How can I integrate Cytoscape into my workflow?
- I want to generate Style for each time point and create
small multiples of networks.

87. cyREST
RESTful API for Cytoscape

88. https://github.com/idekerlab/cy-rest-R/blob/develop/
workflow1_structure_based_visualization.R

89. cyREST and other programming tools for Cytoscape will be covered in
the Advanced Cytoscape Workshop from 3:15PM

90. Interactive Data Analysis
Environments
In-House Databases External Computing Resources
- Graph Layout
- Statistical Analysis
- Data Pre-processing
RStudio
- NumPy
- SciPy
- Pandas
- NetworkX
IPython Notebook
File / Code Hosting ServicesPublic Data Repository
PSICQUIC Services
EBI RDF Platform
Other Bioinformatics Web Applications / Services
- igraph
- rCurl
Command Line Tools
> sed
> awk
> grep
> curl
Web Browsers
Data Repository & Collaboration Service
Data Bus (Internet)
Your Workstation
Cytoscape App Store
Cytoscape Desktop
Apps
Core
REST

91. Interactive Data Analysis
Environments
In-House Databases External Computing Resources
- Graph Layout
- Statistical Analysis
- Data Pre-processing
RStudio
- NumPy
- SciPy
- Pandas
- NetworkX
IPython Notebook
File / Code Hosting ServicesPublic Data Repository
PSICQUIC Services
EBI RDF Platform
Other Bioinformatics Web Applications / Services
- igraph
- rCurl
Command Line Tools
> sed
> awk
> grep
> curl
Web Browsers
Data Repository & Collaboration Service
Data Bus (Internet)
Your Workstation
Cytoscape App Store
Cytoscape Desktop
Apps
Core
REST
→ Service Repository
→ Network Data Repository

92. Service
- Service = ANY program wrapped with REST API
- Examples:
- ID Mapping
- Format converter
- BioPAX to GraphML
- GO Enrichment Analysis

93. Writing CI Services
1. Write a command line tool
2. Wrap it with REST API
3. Register to job manager (provided by us)

94. Why this is important?
In most cases, cutting-edge bioinformatics algorithms are
published as (hard-to-use) command line tools written by
researchers/graduate students
Rewriting it as Cytoscape App is hard
But wrapping it with REST API is not so difficult
Once published as service, it can be called from any
tools, including R/Bioconductor, Python, and Cytoscape

95. Cytoscape
For Desktop Cytoscape 3.4
Publish to the web
For Building Web Applications Cytoscape.js
Interaction Data
Repository
NDEx
Cyberinfrastructure (CI)
Sample Services
Fast ID Mapping
Network Image Generator
Format converter
Data Format CX
Job Router ELSA
Visualization Widgets
Network Widget
Table Widget
Composite Widget NDEx Valet

96. NDEx
Sample Services
Fast ID Mapping
Network Image Generator
Format converter
Data Format CX
Job Router ELSA

99. Computing
Infrastructure
Community

100. Community

102. - Large user and developer community
- Lots of examples and documents
- Workshops / Lectures

103. Community is equally important as technology
for successful CI

104. How to Participate

106. 2016 Keiichiro Ono
kono@ucsd.edu

107. • https://flic.kr/p/bFZpyg
• https://flic.kr/p/bmXUz1
Photo Credits

108. • https://www.flickr.com/photos/23629083@N03/15409436041/in/photolist-ptFotK-9uS2gj-hypkSp-hypk9F-hypjha-99c472-9Xkuuc-huNmqB-7NMxMz-rg2Xh2-qYABcA-qjnGoB-rg2WVF-
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• https://www.flickr.com/photos/nebulux/10000066526/in/photolist-geEXo7-58r1VP-6GioJH-9juEda-53HFiR-4sq7n3-4gyg7e-8ag9VV-8uqK43-4E89Gc-
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• https://www.flickr.com/photos/stratman2/8613731520/in/photolist-e8aChq-7LLUoQ-8s8eBL-6uGRmE-77wKJF-
dqo6ar-6hffGK-7rykRT-6fG8WV-8unyFa-8AeF8A-93Xpo2-9XLXCj-7GVMym-5Tu3dJ-7v58RC-5K9nBF-2MbvpL-2M77nV-et54Ce-6hfgvr-6hffQa-67wNj5-9FDGTz-49NmoE-eFXB7u-76QB7H-
brdbSP-brcYHT-22zYYv-6fFZoM-ckuXNC-a8UZ3D-dzGXYU-6nf4MN-4j7TzA-47fYur-2kutoV-56catX-apUJgr-cSJHkG-88w1ie-6Nbj1a-8MYxve-6xL3SF-6fL87j-4G6x71-
dUL16b-7auq8Q-6hwbVB
• https://www.flickr.com/photos/gcwest/281385801/in/photolist-5mFJtX-4o3Ria-hD9E92-qSbck-9abnoA-7hsWoU-ntEmgy-oSAQtv-nx5Chg-iuZJCa-j7eWKk-hD7JTZ-4iECHX-j8M2r7-bSrWHc-
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