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Transcript of 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
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Thanks for Attending!
You are about to learn modern tools boosting your productivity!
REST
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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
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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
![Page 5: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/5.jpg)
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
![Page 6: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/6.jpg)
Computer Science Biology
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Cytoscape and IPython Notebook for Reproducible Data Visualization Workflow
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Review: Basic Data Visualization Workflow with Cytoscape
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1. Data Integration (Load Networks and Tables)
2. Data Analysis
3. Visualization
Basic Workflow
4. Prepare for Publication
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Network Data
Annotated Networks
Attributes
Analyzed Data
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Cline, Melissa S., et al. "Integration of biological networks and gene expression data using Cytoscape." Nature protocols 2.10 (2007): 2366-2382.
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Cline, Melissa S., et al. "Integration of biological networks and gene expression data using Cytoscape." Nature protocols 2.10 (2007): 2366-2382.
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Results
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Sharing Results
😐
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Sharing Results and Process
😃
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Point & Click Operation is Easy, but not Reproducible…
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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
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Goal: Reproducible Science
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Goal: Reproducible Science
REST
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Tools You Need
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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
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Why ?
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- Full-stack
- Data preparation to web application
- Easy to learn
- Strong support from data science community
- Tons of high-performance libraries
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by Peter Wang @PyData 2014
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But most of the tools are language-agnostic!
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Basic Data Visualization Workflow
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Data Preparation Analysis Visualization
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Data Preparation
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Data Preparation
- Cleansing
- Normalization
- Missing values
- Corrupted values
- Reformat
- Conversion
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Data Preparation Analysis Visualization
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Analysis
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Analysis
- Filtering
- Standard graph statistics
- Density
- Betweenness
- Centrality
- Clustering
- Community Detection
- GO enrichment analysis
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Data Preparation Analysis Visualization
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Visualization
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Visualization
- Mapping
- Data points to visual variables
- Layout
- For graphs:
- Force-directed
- Tree
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Data Preparation Analysis Visualization
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Data Preparation
Analysis Visualization
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Data Preparation
Analysis Visualization
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Data Preparati
on
Analysis Visualization
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REST
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Git/GitHub For Sharing Code/Notebooks
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Git/GitHub For Sharing Code/Notebooks
- Git - Distributed Source Code Management System
- GitHub - (Public) Remote repository + great user interface for working with OSS code
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- Create a new repository from existing one
- Complete copy of the original + your full access
- Pull Request
Forking
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Exercise: Fork Repository
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Prepare Environment to Run Notebooks
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Docker as Portable Data Analysis Environment
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Bare Metal Machine
OSVirtual Machine
Frameworks
Your App
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Bare Metal MachineOS (Linux)
Docker
FrameworksApplication
FrameworksApplication
FrameworksApplication
FrameworksApplication
FrameworksApplication
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What is Docker?
- Container to run applications in an isolated environment
- Application = Layer of images
- Sharable Environments
- Environments as code
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Docker Hub
- Sharing environments as code!
- Dockerfile - Definition of your container
- “GitHub of Images”
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Image B
Image C
Image A
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Data Analyst’s Toolbox
Basic Python
Graph Analysis
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Run a Container
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Quick Start
‣git clone [email protected]: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
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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)
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~/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…
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~/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
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IPython Notebook as your electronic lab notebook
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Jupyter as a Lab Notebook for Dry Experiments
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Interactive Command-Line +
Markdown-based Documents
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IPython Notebook? Jupyter?
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IPython Notebook
Notebook UI
+ Python Kernel
Jupyter Notebook UI
+
Language Kernel
(R/Julia/etc.)
![Page 76: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/76.jpg)
Language-Agnostic
- From next version (4.x), Python Notebook will be an implementation of Jupyter
- You can switch to other language kernels
![Page 77: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/77.jpg)
![Page 79: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/79.jpg)
Let’s start: Lesson 0
![Page 81: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/81.jpg)
• https://flic.kr/p/bFZpyg
• https://flic.kr/p/bmXUz1
Photo Credits
![Page 82: SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook](https://reader030.fdocuments.net/reader030/viewer/2022032420/55a5c92e1a28abe1308b46d0/html5/thumbnails/82.jpg)
• 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