The document discusses building reproducible network data analysis and visualization workflows using REST APIs and containerization. It aims to solve problems with complex software stacks that are difficult to set up and not reproducible. The goal is to create reproducible and scalable "dry experiments" using Docker containers, GitHub for source code sharing, Jupyter notebooks as electronic lab notebooks, and the cyREST module for the Cytoscape network analysis software. Examples of scenarios using local workstations and cloud computing are presented, as well as a demo and future plans.

1. Keiichiro Ono
UCSD Trey Ideker Lab
Cytoscape Core Team
Lab Meeting
Aug 4, 2015
Building Reproducible Network Data Analysis / Visualization Workflows
REST

2. Problems We are Trying to Solve
- Complex software stack for data analysis
- Setting up environment for data analysis is not trivial, and it is time-
consuming
- Python 3.x or 2.x/NumPy/SciPy/Cython Modules
- R/Bioconductor/packages
- OS version, etc.
- Automation
- Point-and-Click operations are not reproducible
- Applying different layouts to 100 networks by hand is possible, but ridiculous
- Sharing Recipe (= common workflows) is hard
- Integration to external computing resources

3. Goal: Reproducible,Scalable Dry Experiments
REST

4. REST
- Docker
- Data analysis environment in a portable container
- GitHub
- Source code sharing
- Jupyter Notebook
- Your electronic lab notebook
- cyREST
- RESTful API module for Cytoscape
Goal: Reproducible, Scalable Dry Experiments

5. Data
Preparation
Analysis Visualization

6. REST
Scenario 1: Everything on your Workstation
Notebook Server
Your Jupyter Notebook

7. REST
Scenario 2: Workstation + Cloud
Notebook Server
Your Jupyter Notebook

8. Example: Community-Detection + Edge-Weighted Layout
Source Code: bit.ly/1P4LUFU

9. Demo

10. TODO
- Integration to Cyberinfrastructure (CI)
- R Wrapper
- https://github.com/tmuetze/
Bioconductor_RCy3_the_new_RCytoscape
- More realistic workflows / pipelines

11. Resources
- cyREST
- http://apps.cytoscape.org/apps/cyrest
- py2cytoscape
- https://pypi.python.org/pypi/py2cytoscape
- RCy3
- https://github.com/tmuetze/
Bioconductor_RCy3_the_new_RCytoscape