sdcsb advanced tutorial: reproducible data visualization workflow with cytoscape and ipython...
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SDCSB Advanced Cytoscape Tutorial
4/17/2015 @Sanford
Keiichiro Ono UCSD Trey Ideker Lab Cytoscape Core Team
Building Reproducible Network Data Visualization Workflows with Cytoscape and IPython Notebook
Thanks for Attending!
You are about to learn modern tools boosting your productivity!
REST
Keiichiro Ono
BackgroundBioinformatics
Computer ScienceWork
ResearchBioinformatics workflow
Visualization pipeline
Data
VisualizationNetworks
Other Biological Data
Integration
Molecular Interactions
Pathways
Annotations
Software Development
CytoscapeNeXO
Cyberinfrastructure
All kinds of small tools
Like
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Mondrian
Music
Electronica
TechnoMinimal
Detroit
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Sci-fiMovie
Novel
Life
US
San DiegoSan Francisco Bay Area
Los Angeles
Orange County
JapanGifu
Tokyo
Keiichiro Ono
BackgroundBioinformatics
Computer ScienceWork
ResearchBioinformatics workflow
Visualization pipeline
Data
VisualizationNetworks
Other Biological Data
Integration
Molecular Interactions
Pathways
Annotations
Software Development
CytoscapeNeXO
Cyberinfrastructure
All kinds of small tools
Like
ArtKandinsky
Mondrian
Music
Electronica
TechnoMinimal
Detroit
Jazz
Sci-fiMovie
Novel
Life
US
San DiegoSan Francisco Bay Area
Los Angeles
Orange County
JapanGifu
Tokyo
Keiichiro Ono
BackgroundBioinformatics
Computer ScienceWork
ResearchBioinformatics workflow
Visualization pipeline
Data
VisualizationNetworks
Other Biological Data
Integration
Molecular Interactions
Pathways
Annotations
Software Development
CytoscapeNeXO
Cyberinfrastructure
All kinds of small tools
Like
ArtKandinsky
Mondrian
Music
Electronica
TechnoMinimal
Detroit
Jazz
Sci-fiMovie
Novel
Life
US
San DiegoSan Francisco Bay Area
Los Angeles
Orange County
JapanGifu
Tokyo
Computer Science Biology
Cytoscape and IPython Notebook for Reproducible Data Visualization Workflow
Review: Basic Data Visualization Workflow with Cytoscape
1. Data Integration (Load Networks and Tables)
2. Data Analysis
3. Visualization
Basic Workflow
4. Prepare for Publication
Network Data
Annotated Networks
Attributes
Analyzed Data
Cline, Melissa S., et al. "Integration of biological networks and gene expression data using Cytoscape." Nature protocols 2.10 (2007): 2366-2382.
Cline, Melissa S., et al. "Integration of biological networks and gene expression data using Cytoscape." Nature protocols 2.10 (2007): 2366-2382.
Results
Sharing Results
😐
Sharing Results and Process
😃
Point & Click Operation is Easy, but not Reproducible…
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
Goal: Reproducible Science
Goal: Reproducible Science
REST
Tools You Need
REST
- Docker - Data analysis environment in a portable
container
- GitHub - For source code sharing
- IPython Notebook - Your electronic lab notebook
- cyREST - RESTful API module for Cytoscape
Why ?
- Full-stack
- Data preparation to web application
- Easy to learn
- Strong support from data science community
- Tons of high-performance libraries
by Peter Wang @PyData 2014
But most of the tools are language-agnostic!
Basic Data Visualization Workflow
Data Preparation Analysis Visualization
Data Preparation
Data Preparation
- Cleansing
- Normalization
- Missing values
- Corrupted values
- Reformat
- Conversion
Data Preparation Analysis Visualization
Analysis
Analysis
- Filtering
- Standard graph statistics
- Density
- Betweenness
- Centrality
- Clustering
- Community Detection
- GO enrichment analysis
Data Preparation Analysis Visualization
Visualization
Visualization
- Mapping
- Data points to visual variables
- Layout
- For graphs:
- Force-directed
- Tree
Data Preparation Analysis Visualization
Data Preparation
Analysis Visualization
Data Preparation
Analysis Visualization
Data Preparati
on
Analysis Visualization
REST
Git/GitHub For Sharing Code/Notebooks
Git/GitHub For Sharing Code/Notebooks
- Git - Distributed Source Code Management System
- GitHub - (Public) Remote repository + great user interface for working with OSS code
- Create a new repository from existing one
- Complete copy of the original + your full access
- Pull Request
Forking
Exercise: Fork Repository
Prepare Environment to Run Notebooks
Docker as Portable Data Analysis Environment
Bare Metal Machine
OSVirtual Machine
Frameworks
Your App
Bare Metal MachineOS (Linux)
Docker
FrameworksApplication
FrameworksApplication
FrameworksApplication
FrameworksApplication
FrameworksApplication
What is Docker?
- Container to run applications in an isolated environment
- Application = Layer of images
- Sharable Environments
- Environments as code
Docker Hub
- Sharing environments as code!
- Dockerfile - Definition of your container
- “GitHub of Images”
Image B
Image C
Image A
Data Analyst’s Toolbox
Basic Python
Graph Analysis
Run a Container
Quick Start
‣git clone git@github.com:idekerlab/sdcsb-advanced-tutorial.git
‣cd sdcsb-advanced-tutorial
‣docker run -d -v $PWD:/notebooks -p 80:8888 -e "PASSWORD=yourpass" -e "USE_HTTP=1" idekerlab/vizbi-2015
docker run -d -v $PWD:/notebooks -p 80:8888 -e "PASSWORD=yourpass" -e "USE_HTTP=1" idekerlab/vizbi-2015
Actual Command to Run the Image (one-line)
~/g/sdcsb-advanced-tutorial git:master ›❯›❯›❯ docker run -d -v $PWD:/notebooks -p 80:8888 -e "PASSWORD=sdcsb" -e "USE_HTTP=1" idekerlab/vizbi-2015 Unable to find image 'idekerlab/vizbi-2015:latest' locally Pulling repository idekerlab/vizbi-2015 7dfae1b52000: Pulling dependent layers 511136ea3c5a: Download complete f3c84ac3a053: Download complete a1a958a24818: Download complete 9fec74352904: Download complete d0955f21bf24: Download complete 4f527ba3fd02: Download complete ac7605e8bbf0: Download complete 8e8747f25e33: Download complete . . .
This takes a very long for the first time…
~/g/sdcsb-advanced-tutorial git:master ›❯›❯›❯ docker ps -a CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES fa3a9466a261 idekerlab/vizbi-2015:latest "/notebook.sh" 3 minutes ago Up 3 minutes 0.0.0.0:80->8888/tcp sad_wright
Check Status
IPython Notebook as your electronic lab notebook
Jupyter as a Lab Notebook for Dry Experiments
Interactive Command-Line +
Markdown-based Documents
IPython Notebook? Jupyter?
IPython Notebook
Notebook UI
+ Python Kernel
Jupyter Notebook UI
+
Language Kernel
(R/Julia/etc.)
Language-Agnostic
- From next version (4.x), Python Notebook will be an implementation of Jupyter
- You can switch to other language kernels
Let’s start: Lesson 0
• 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
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