Friday, 4/17/2015 at Sanford
by Keiichiro Ono (UCSD Trey Ideker Lab)
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.
This tutorial is designed to learn the following topics:
You don't have to worry too much about Python. Building simple data analysis workflows requires only basic knowledge of Python.
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:
Again, if you use the Docker container we provide, you don't have to install any of these.
Please send email to me (kono at ucsd edu)