This document summarizes Keiichiro Ono's lab meeting presentation about developing a RESTful API for Cytoscape. The presentation covered the motivation for external tools to programmatically access Cytoscape, the design of a new Cytoscape module that exposes a RESTful API, and a proof-of-concept demo. The goal is to make Cytoscape more accessible for hardcore users to embed in automated workflows from languages like R and Python.

1. Keiichiro Ono
UC, San Diego
Lab Meeting 4/21/2014
Cytoscape and
External Tools

2. Agenda
- Background
- Why external tools?
- New Cytoscape Module:
RESTful API for Cytoscape
- Current design
- Proof-of-concept demo
- Future plan

3. Problems

4. Problems
- Cytoscape is getting more and more user-friendly
- Lots of GUI-based Apps
- Easy access to interaction databases
- But not hardcore-user-friendly!
- There is no easy way to embed Cytoscape as a part of
larger, automated workflow (using R/Python/etc.)
- We are losing hardcore users (like you) because of this
limitation…

5. THE SMALL TOOLS MANIFESTO FOR BIOINFORMATICS
- Every single tool should do the smallest possible task really well
- Every single tool lives in its own public source code repository
- All tools are free and open source software (FOSS) and come with a
license approved by the Free Software Foundation (FSF).
- Source code should be easy to read and understand by any
competent software developer
- Error conditions and exceptions should be descriptive and handled
in a clear way
- When possible tools should support (Unix) pipes
- When possible tools provide a useful command line interface
- Tools should avoid system dependencies, such as named (absolute)
file paths
- Every single tool comes with a simple build protocol, at least for
Linux
- Software installation and deployment dependencies are handled
through external package management system
https://github.com/pjotrp/bioinformatics

6. Data Analysis
Tool Ecosystem

7. Network Data Analysis
Analysis
Visualization

8. Network Data Analysis
Analysis
s
Visualization
Desktop
Gephi
Cytoscape
matplotlib
Cytoscape.js

9. Network Dat
Analysis
Graph Analysis
NetworkX
igraph
Cytoscape
Python
Pandas
NumPy
SciPy
Excel
IPython
3rd Party Apps
NetworkAnalyzer

10. Network Data Analysis
Analysis
Graph Analysis
NetworkX
igraph
Cytoscape
Python
Pandas
NumPy
SciPy
Excel
Visualization
Desktop
Gephi
Cytoscape
matplotlib
Web
Cytoscape.js
sigma.js
d3
NDV3
d3.chart
Google Charts
Data Storage
Graph
Neo4j
GraphX
Document
MongoDB
Relational
MySQL
IPython
3rd Party Apps
NetworkAnalyzer

11. http://visualizing.jp/d3-unconf-2014-2/

12. Tools We Will Support
Analysis VisualizationData Preparation

13. Data Exchange

14. Data I/O
- Should be platform-independent
- Need to support multiple environments
- R, Python w/Pandas, MATLAB, Perl, Shell Scripts, or
workflow engine like Kepler/Taverna
- RESTful API
➡ Access Cytoscape data and functions via HTTP, which
is supported by virtually all platforms

15. RESTful API
- Example
- GET http://localhost:9000/networks
➡ Returns all networks in machine-readable format
- GET http://localhost:9000/networks/52
➡ Returns a network with ID 52
- POST http://localhost:9000/networks
➡ Create a new network from the data

16. CRUD
Resource POST (Create) GET (Read) PUT (Update) DELETE
(Delete)
/networks Create a new
network
List all networks Bulk update
network data
Delete all
networks
/networks/SUID Error Show all
information for
the network with
SUID
Update
information for
the network with
SUID
Delete network
with SUID

17. Demo

18. Data Formats
YJR022W pp YOR167C
YJR022W pp YLR264W
YJR022W pp YNR053C
YER116C pp YDL013W
YNL307C pp YAL038W
YNL216W pd YCR012W
YNL216W pd YGR254W
YNL216W pd YHR174W
YNL216W pd YIL133C
YNL216W pd YLR044C
YNL216W pd YOL120C
YNL216W pd YNL301C
YNL216W pd YCL030C

19. Which Format Should We Support? (1)
- Basic data exchange format in RESTful world
- JSON (JavaScript Object Notation)
- Like XML, not an actual format, just a standard
- For the first version, we will use Cytoscape.js
style JSON

22. Which Format Should We Support? (2)
- Other File Formats
- Networks: GraphML, EdgeList, Adj. Matrix
- Tables: CSV/TSV
- Open Question:
Conversion from Standard Data Structure
- igraph object to JSON
- DataFrame to JSON/CSV

23. Long-Term Goal: Cytoscape Cyberinfrastructure
Internet
Service 1 Service 2
NDEx (DB)
Web Browser
Cytoscape Desktop

24. 2014 Keiichiro Ono
kono@ucsd.edu