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Wednesday Oct. 14, 2020, 5 p.m.–Oct. 14, 2020, 5:15 p.m. in Jupyter in Scientific Research

Automating biological network visualization with Jupyter Notebook

Kozo Nishida

Audience level:

Brief Summary

Cytoscape is the de facto standard software for biological network visualization. Cytoscape is mainly used as stand-alone desktop software. On the other hand, it has a REST server function and can be controlled with HTTP requests. In this talk, I will introduce how to use Cytoscape and Jupyter Notebook together as a biological visualization workflow automation system.


Introductions to Cytoscape and biological network visualization

Motivations for the automation of the biological network visualization workflow

The workflow system that combines Jupyter Notebook and Cytoscape


Central thesis

Biological network visualization workflow can be automated and reproducible with Jupyter Notebook

Key takeaways

What background knowledge is expected from the attendees

Source code