JupyterCon 2020 - Presentation: Automating biological network visualization with Jupyter Notebook

What is Cytoscape?
- Cytoscape is a highly customizable network visualization software.
- The styling feature according to the values assigned to nodes and edges is particularly useful to create figure for research paper.
Biological network visualization
- It is a network in which molecules are represented by nodes and interactions between molecules are represented by edges. The nodes and edges have biological quantitative values.
- In the visualization workflow, various software and data are used to give the quantitative values to the network.
- An implementation of such a workflow for Cytoscape is called an “App”.
Creating a Cytoscape App
- App has been written in Java mainly for GUI operation.

Why automation?
- GUI operation is manual and time consuming.
- Cytoscape has REST service and can be controlled with HTTP requests.
- By using REST service, the workflow can be automated with Python or R instead of Java.
- Automation of the operation improves the research reproducibility.
Why Jupyter Notebook?
- Writing workflows in Jupyter Notebook improves their reproducibility.
- With Binder or Google Colab, anyone can learn the workflow interactively and check the reproducibility.

RCy3 and py4cytoscape: REST service wrapper library for compatibility with Python and R packages

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

There's still room to leverage Jupyter Notebook to improve biological workflows.
You can use Jupyter Notebook to automate the manual operation of desktop software and it can improve the reproducibility of scientific workflow.

Automating biological network visualization with Jupyter Notebook