SDCSB Cytoscape Workshop

Advanced Cytoscape: Cytoscape, IPython, Docker, and reproducible network data visualization workflows

Friday, 4/17/2015 at Sanford

by Keiichiro Ono (UCSD Trey Ideker Lab)

Welcome!

Background

Welcome to the Advanced Cytoscape tutorial session! Cytoscape is a powerful tool for biological network data analysis and visualization and it is a de-facto standard tool in systems biology community. However, no one can complete their data visualization workflow only with a tool. In fact, there is no one-size-fits-all type tool for modern biology. This means there is a need to glue multiple tools and make them work nicely together to visualize complex data sets. Python is a perfect programming language for this purpose. In this tutorial, we will use IPython Notebook as an electronic lab notebook for your data analysis and visualization workflow with Cytoscape.

Goals

This tutorial is designed to learn the following topics:

  • Basics of IPython Notebook
    • Navigation
  • Cytoscape RESTful API basics
    • Import/create networks
    • Create Visual Styles
    • Using external web services
  • Data visualization with IPython Notebook and Cytoscape
    • Generate reusable Styles with Python
    • Embed interactive visualization using cytoscape.js widget

Prerequisites

  • Basic knowledge of RESTful API
  • Basic Python skill - only basics, such as conditional statements, loops, basic data types.
  • Basic knowledge of Cytoscape
    • Cytoscape data types - Networks, Tables, and Styles.

You don't have to worry too much about Python. Building simple data analysis workflows requires only basic knowledge of Python.

About Docker

All required software packages to run these lessons are packed in Docker container for your convenience. Docker is a powerful tool to make your workflow reproducible, but it is not the main forcus of this course. I strongly recommend to use Docker to run your notebook server, but if you want to build on your machine, install the following to try these notebooks:

  • Python 3
  • IPython Notebook
  • requests
  • py2cytoscape
  • pandas
  • NetworkX

Again, if you use the Docker container we provide, you don't have to install any of these.

Tutorials

Questions?

Please send email to me (kono at ucsd edu)