1. Cytoscape
An open-source ecosystem for complex
network analysis and visualization
Kei Ono
kono@ucsd.edu
The Cytoscape Consortium/
UC,San Diego Dept.of Medicine
Bioinformatics Software Engineer
3. A gene ontology inferred from molecular networks. Dutkowski J,
Kramer M,Surma MA,Balakrishnan R,Cherry JM,Krogan NJ,Ideker
T., Nature Biotechnology 2013 Jan;31(1):38-45.
NeXO Web: the NeXO ontology database and visualization
platform. Dutkowski J, Ono K,Kramer M, Yu M, Pratt D,Demchak B,
Ideker T., Nucleic Acids Res. 2014 Jan;42(Database issue).
4. Using deep learning to model the hierarchical structure and function of a cell.
Ma J,Yu MK,Fong S,Ono K,Sage E,Demchak B,Sharan R,Ideker T. Nat Methods. 2018 Mar 5. doi: 10.1038/
nmeth.4627.PMID: 29505029
24. Cytoscape = Ecosystem
= Collection of applications and libraries
for network analysis and visualization
25. REST API Support
• Language-agnostic
• Enable users to automate
their workflows
• Works nicely with other
popular tools:
• igraph
• NetworkX
• Graphviz
• graph-tool
https://cytoscape.org/cytoscape-tutorials/presentations/advanced-automation-2018-sib.html#/