Presentation slides for SDCSB Cytoscape Workshop on 5/19/2016. The presentation contains current status of Cytoscape project and overview of the Cytoscape ecosystem. It briefly mentions the Cytoscape Cyberinfrastructure.
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
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
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
32. App Collections
• Users can install multiple
Apps at once
• Organized for specific use
cases
• Mass Spec
• Omics Analysis
• Functional Enrichment
• EmrichmentMap
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
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
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
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
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
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
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
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
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
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
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.
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