Introduction to iPython Notebook

R. Burke Squires

NIAID Bioinformatics and Computational Biosciences Branch (BCBB)

Python Programming for Scientists Series

• Introduction to iPython Notebook
• Introduction to Python Programming
• Introduction to Biopython Programming
• Introduction to Data Analysis with Python

NIAID Bioinformatics and Computational Biosciences (BCBB)

Yentram Huyen, Ph.D., Chief

Major Areas of Research

• Computational biology collaboration and training
• Bioinformatics software development
• Biocomputing resources

Personnell

• Computational biologists (Consultants)
• Scientific programmers
• Program managers

Introduction to iPython Notebook

Outline

Materials take from IPython tutorial found here

Download the examples folder to the same folder as here and the link below will work.

• Notebook:The IPython Notebook frontend
  • What is the IPython Notebook?
  • Running the Notebook Server
  • Notebook Basics
  • Running Code
  • Working With Markdown Cells
• Kernel:IPython's core syntax and command line features available in all frontends
  • Cell Magics
  • Script Magics
  • Rich Output
  • Custom Display Logic
  • Plotting in the Notebook
  • Capturing Output
• Parallel Computing: IPython's library for interactive parallel computing
  • Basics
• Data visualization in iPython Notebooks
  • Matplotlib: Static data visualization with matplotlib (Download Lecture-4-Matplotlib.ipynb)
  • Bokeh: Dynamic data visualization with bokeh

Additional iPython Notebook Examples:

http://nbviewer.ipython.org