Crash Course: Python Scripting for Biochemistry & Molecular Biology


Tuesday, February 22nd 2022 • 1:00 PM EST

Registration (required):



This IQB Crash Course is a programming workshop designed to introduce life scientists to the power and flexibility of solving problems with Python. It is designed to move users beyond a "plug-and-play" approach that is based on spreadsheets and web applications in their teaching and research to writing scripts to parse large collections of data and to perform dynamic calculations. The live-coding workshop is designed to introduce specific coding skills, as well as provide insight into the broader array of open-access resources and libraries that are available for scientific computation.

Each live coding segment will be followed by a hands-on programming exercise to introduce you to the programming language and to help you identify the challenges associated with coding. You will learn to extract data from PDB files, first by working with one file to learn one set of tools, then by using a different set of tools to explore, sort and output results from a large number of files.

For those who are interested, a 12-hour workshop will be offered in July, 2022.

Program | Download Printable Program

1:00–1:05 pm
Stephen K. Burley, M.D., D.Phil.: Founding Director, Institute for Quantitative Biomedicine
1:05–1:10 pm

Welcome and Crash Course Learning Objectives
Paul A. Craig, Ph.D., Professor of Biochemistry, Rochester Institute of Technology

Jessica A. Nash, Ph.D., Software Scientist, Molecular Sciences Software Institute

1:10–2:00 PM

Lesson 1: Introduction to Python and to Jupyter Notebooks
Paul A. Craig

2:00–2:10 pm

Hands-on Exercise 1
Paul A. Craig and Jessica A. Nash

2:10–2:20 pm

Questions and Answers about Exercise 1

2:20–3:00 pm

Lesson 2: Reading and Writing Files
Jessica A. Nash

3:00-3:10 pm

Hands-on Exercise 2
Jessica A. Nash and Paul A. Craig

3:10-3:20 pm

Questions and Answers about Exercise 2

3:20-3:30 pm 


3:30-4:00 pm  

Processing Multiple Files
Paul A. Craig

4:00-4:20 pm  

Hands-on Exercise 3
Paul A. Craig and Jessica A. Nash


4:20-4:50 pm 

Visualizing structures in the Jupyter Notebooks
Jessica A. Nash

4:50-5:00 pm 

Hands-on Exercise 4
5:00 pm  Closing Remarks and Acknowledgments
Stephen K. Burley



Paul A. Craig, Ph.D., Professor of Biochemistry                                           Jessica A. Nash, Ph.D., Software Scientist
Rochester Institute of Technology                                                        Molecular Sciences Software Institute               



RCSB Protein Data Bank                                                                                Institute for Quantitative Biomedicine (IQB)