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What’s New In Cytoscape? Keiichiro Ono UCSD Trey Ideker Lab Cytoscape Core Team SDCSB Workshop 4/17/2015 @Sanford
| Date post: | 15-Jul-2015 |
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What’s New In Cytoscape?
Keiichiro Ono UCSD Trey Ideker Lab Cytoscape Core Team
SDCSB Workshop 4/17/2015 @Sanford
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-)
Quick Introduction to Cytoscape
What is Cytoscape?
An Open Source Platform for Biological Network Data Integration, Analysis and Visualization
Cytoscape
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
Cytoscape Projects
Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)
Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)
Cytoscape 3.2
Cytoscape 3.2- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes
Cytoscape 3.2- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes
Chart Editor
Chart Editor
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
Gradient Editor
Cytoscape 3.2- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes
Background
Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)
Cytoscape and Web Technologies
History
10 Years Ago…
2005
- Cytoscape 2.2: a Java Desktop Application
- Google released an application called Google Maps beta
- “Re-discovery” of JavaScript, or Ajax
Today
Today
- JavaScript is a programming language for serious application
- Web is a competitive application platform
What should we do?
- Cytoscape should support use cases such as:
- Sharing data over the web
- Visualize network data on the web browser
cytoscape.js
- A JavaScript Library
- NOT A WEB APPLICATION!
- For web application programmers
- But there are some web applications using Cytoscape.js
cytoscape.js
Web Apps using Cytoscape.js
cynetshareA web application using cytoscape.js
bit.ly/1DNmetV- Location of Network File
- Visual Style
- Zoom Level
- Viewable Area
Publication Viewer
Interactive paper figuresCollaboration Project with Elsevier
Cytoscape 3.2- Latest version of Cytoscape
Desktop application
- New Features:
- Chart Editor
- Export as Web Application
- Performance Improvements
- Lots of bug fixes
Export as Web Application
Export as Web Application
Exporting Cytoscape-generated visualizations as a complete web application using Cytoscape.js
Demo
Cytoscape Projects
- Cytoscape 3.2.1
- Cytoscape and Web
- Cytoscape Cyberinfrastructure (CI)
Cytoscape Cyberinfrastructure
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
Basic Workflow of Data Visualization
Data Preparation
Analysis Visualization
ALL tools should work nicely together with other popular software packages!
as a service
REST
cyREST for Cytoscape-as-a-service
Users
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.
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.
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…
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.
REST
What is cyREST?
- Platform-independent, RESTful API module for Cytoscape
- In short, you can drive Cytoscape from any programming languages
REST
REST
Cytoscape 3.1+Clients
POST
PUT
DELETE
GET
Get full network with unique ID 52 as JSON
GET http://localhost:1234/v1/networks/52
Cytoscape CyberinfrastructureCytoscape CI: a long-term goal
Cyberinfrastructure?
–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
?
Computing Infrastructure Community
App Store
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
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
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
• https://flic.kr/p/bFZpyg
• https://flic.kr/p/bmXUz1
Photo Credits
• https://www.flickr.com/photos/23629083@N03/15409436041/in/photolist-ptFotK-9uS2gj-hypkSp-hypk9F-hypjha-99c472-9Xkuuc-huNmqB-7NMxMz-rg2Xh2-qYABcA-qjnGoB-rg2WVF-rdQYMf-qjaxy7-rg5Aoo-rg2Wre-qYAAt1-rg2Wev-qYAAaA-rg2W1V-rdQXT1-qjawtS-rg9ePH-rg5zb3-qjnEtV-qYHAvc-qYBA9d-rg2V7F-qYHAeF-qYAySA-rg5ys9-rg9dLF-rg2Utg-rg9drH-qYAyew-rg9dmc-rg5xP5-rg5xDA-qYAxV5-rg2TLe-rg5xp7-rg5xfQ-aq32tC-hba7em-hbafzE-gbeABq-gck7Dv-7PoYg1-fkisQL
• https://www.flickr.com/photos/nebulux/10000066526/in/photolist-geEXo7-58r1VP-6GioJH-9juEda-53HFiR-4sq7n3-4gyg7e-8ag9VV-8uqK43-4E89Gc-iWDeiJ-9G47M4-9G71KC-9waYuP-5FWSrX-87Mhxi-9G71XY-7Ai8hs-48vd2B-7B7o6n-6D9uWd-6hffXv-gYExNx-7defC1-66ygvB-4LsWSN-6D5n5k-6hfg5z-eucXAh-8uyuuG-aAY6cH-76QCEX-7f6mdp-RntfW-eFuVBC-5nY8Vc-7utTA2-brdj8F-92k6n3-5KdCfh-83uVKy-8unxG8-3d3zxi-cdz8S7-4HT5qQ-99SwEn-7Akbcb-8y7ds9-fvo9zH-9zZky3
• 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-prpFcX-db7xd-jLmzoF-75mqRx-pnSzL-6gVcao-9F5bop-j77HEs-73Umq1-5kRyNp-hD9cR2-mTvNB8-gyXWaf-Lkro7-idQBY4-fRYu1-5eR2cn-3EK4k-nnxH8u-9uDMLx-4NY3Yi-kDQagt-ioGRSb-75qid1-82RzYt-5qQuwt-n8hvL6-ifemz5-3iYUQG-aJnNiX-mzirX2-23rDNy-qx3KEd-h5UnGW-hD7Jqz
