1. What’s New In Cytoscape?
Keiichiro Ono
UCSD Trey Ideker Lab
Cytoscape Core Team
SDCSB Workshop
4/17/2015 @Sanford

2. Welcome!
- This Section:
- Cytoscape Updates
- Cytoscape and the Web
- Working with External Tools and Cytoscape CI
- Afternoon Sessions:
- Cytoscape Workshops: Beginners & Advanced (1:30PM-3:00PM)
- Cytoscape Clinic (3:00PM-)

3. Quick Introduction to
Cytoscape

4. What is Cytoscape?

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

7. 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

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

9. Cytoscape Projects

10. Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)

11. Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)

12. Cytoscape 3.2

13. Cytoscape 3.2
- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes

14. Cytoscape 3.2
- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes

15. Chart Editor

16. Chart Editor

17. Chart Editor
- Visualize multiple data points
to a single view
- Time series data
- Multiple GO terms
- Chart types: Bar, Box, Pie,
Heat Map, Ring
- Part of standard Visual Style
Editor
- Everything will be saved
into session files

18. Gradient Editor

19. Cytoscape 3.2
- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes

20. Background

21. Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)

22. Cytoscape and Web Technologies

23. History

24. 10 Years Ago…

26. 2005
- Cytoscape 2.2: a Java Desktop Application
- Google released an application called
Google Maps beta
- “Re-discovery” of JavaScript, or Ajax

27. Today

29. Today
- JavaScript is a programming language for
serious application
- Web is a competitive application platform

30. What should we do?
- Cytoscape should support use cases such as:
- Sharing data over the web
- Visualize network data on the web browser

31. cytoscape.js

32. - A JavaScript Library
- NOT A WEB APPLICATION!
- For web application programmers
- But there are some web
applications using Cytoscape.js
cytoscape.js

34. bit.ly/1JEAaHj

35. Web Apps using Cytoscape.js

36. cynetshare
A web application using cytoscape.js

39. bit.ly/1DNmetV

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

41. Publication Viewer
Interactive paper figures
Collaboration Project with Elsevier

43. Cytoscape 3.2
- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes

44. Export as Web Application

45. Export as Web Application
Exporting Cytoscape-
generated visualizations as a
complete web application
using Cytoscape.js

49. Demo

50. Cytoscape 3.2.1
www.cytoscape.org/download.php

51. Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)

52. Cytoscape Cyberinfrastructure

53. 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)
- Complex Data Analysis Pipeline
- Need to build pipeline by connecting multiple resources, or services
- Needs for complex, customized data visualization
- Reproducibility
➡ But building, deploying, and maintaining reproducible pipeline is not
straight-forward

54. Basic Workflow
of Data Visualization

55. Data
Preparation
Analysis Visualization

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

57. as a service

58. REST
cyREST for Cytoscape-as-a-service

59. Users

60. User Type I
- Domain experts
- Average computing skills
- Use Excel as their primary
workbench for data analysis
- For them, bioinformatics
means using some of NCBI/
EBI web tools or DAVID
- Have tons of data not analyzed
/ visualized yet
- Excel is my friend.

61. User Type II
- Computational biologists
- Advanced computing skills
- Use Python + SciPy /
NumPy, R + Bioconductor,
or MATLAB every day
- If necessary, write their
own packages
- Use HPC technologies a lot
- Manual operation is evil.

62. Both of them are Important!
- Type I: “Bench Biologists”
- Domain experts
- Data producers
- Type II: Computational Biologists
- Experts of large-scale data analysis
- Especially important for genome-scale
data analysis
They are not well
supported for a long time in
Cytoscape community…

63. Requests from Type II Users
- 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.

64. REST

65. What is cyREST?
- Platform-independent, RESTful
API module for Cytoscape
- In short, you can drive Cytoscape
from any programming languages
REST

66. REST
Cytoscape 3.1+
Clients
POST
PUT
DELETE
GET

67. Get full network with unique ID 52 as JSON
GET http://localhost:1234/v1/networks/52

68. Cytoscape Cyberinfrastructure
Cytoscape CI: a long-term goal

69. Cyberinfrastructure?

70. –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

71. ?

72. Computing
Infrastructure
Community

73. App Store

74. App Store
- Both Cytoscape and Bioconductor have
- Large user and developer community
- Lots of examples and documents
- Workshops
- Community is equally important as technology for
successful CI

75. 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

76. 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

77. 2015 Keiichiro Ono
kono@ucsd.edu

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

79. • 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-
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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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