q-bio Summer School and Conference, 2022

0.1 – Welcome to Python (William Raymond)

Lecture 0.1

Title: Tutorial — Welcome to Module 0

Lecturer: Will Raymond

Lecturer Website: https://www.engr.colostate.edu/~munsky/

Lecturer Email: wsraymon@rams.colostate.edu

Learning Objectives:

      • Learn how to define different variable and data types in Python
      • Learn basics for how to write functions and create notebooks in Python
      • Learn how to read and write data to files using Python
      • Learn how to make and save plots
      • Learn how to search for Python libraries to find and load different biosimulation or bioinformatic tools 

Will Raymond graduated in May 2017 from Colorado State University with a Bachelors in Biomedical Engineering and a Bachelors in Chemical and Biological Engineering.

Will has been a PhD student in Dr. Munsky’s lab since 2019 working on a myriad of projects. He is currently the lead developer on the rSNAPsim, an open source Python TASEP mRNA simulation package. In addition to that, he also works on implementing machine learning for nascent chain tracking fluorescent spot identification. Additionally, a recent area of focus has been modeling tRNA abundances and their effect on translation dynamics.

His primary area of interest is the intersection of machine learning, bioinformatics, and RNA biology. He is most excited about novel ncRNA discovery and advancements in RNA structural identification and disease classification. 

Title: Welcome to Module 0

Abstract: This module is an introduction to some of the basics of Python. Students will learn built in some data types, logic and looping syntax, using NumPy and Pandas, saving I/O, and visualization with matplotlib. Additionally there is a notebook about some of the functionalities of using a Google Colab to run and share you’re code. This section is not a comprehensive Python education, but just enough to get started and to understand the rest of the summer school codes provided.

Suggested Reading or Key Publications:

Links to Relevant Software: 

    • What character is used to denote the built in type of a Python list? How about for a tuple and for a dictionary?
    • How does python denote that a code block is within a logic loop (like a for loop?)