Introduction to Biological Network Analysis and Visualization with Cytoscape Keiichiro Ono Cytoscape Core Developer Team UC, San Diego Trey Ideker Lab / National Resource for Network Biology 5/12/2016 The Scripps Research Institute Lecture 2: Reproducible Workflows with Jupyter Notebook
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Introduction to Biological Network Analysis and Visualization with Cytoscape Part 2
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Introduction to Biological Network Analysis and Visualization with Cytoscape
Keiichiro OnoCytoscape Core Developer TeamUC, San Diego Trey Ideker Lab / National Resource for Network Biology
5/12/2016 The Scripps Research Institute
Lecture 2: Reproducible Workflows with Jupyter Notebook
Problems- Reproducibility of biological research, especially for in vivo/vitro
experiments, is a hard problem
- But this is true even for in silico analysis! - OS version - Revision of scripts - Data analysis software versions - Version of data files - Command line parameters written on a paper napkin - “Black magic” only a grad student knows
- This is something we need to fix, using latest technologies and best practices
Typical 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
Cytoscape for Interactive Visualization
Python for Data Manipulation / Analysis
Lab Notebook for in silico 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
- In this lecture, we will use Python, but you can use language of your choice to control Cytoscape
Question
• Cytoscape is a desktop application
• Point & click GUI operation
• Easy to use, but how can we make our workflow reproducible?
REST
What is cyREST?
- Platform-independent, RESTful API module for Cytoscape - Means you can access basic Cytoscape data objects
programmatically - Now it’s a Cytoscape Core feature!
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