Workshop Description

This workshop will cover the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases. The following is a daily schedule:

Day 1

Slides for day 1 can be found here.

1: Intro and Variables
Video

2: Numbers and Strings
Video

3: True/False and If statements
Video

4: Our First Functions
Video

5: Writing Function in a Text Editor
Video

Day 2

Slides for day 2 can be found here.

6: Dictionaries
Video

7: TipCalculator.py
Video

8: Tip Calculator 2 and For Loops
Video

9: Reverse Complement
Video

10: Reverse Complement with Dictionaries
Video

11: While Loops and Errors
Video

Day 3

Slides for day 3 can be found here.

12: Error Handling
Video

13: Writing a Statistics Module
Video

14: List Comprehension
Video

15: Lambda Cunctions
Video

16: File Input and Output
Video

17: Finding adapter sequences in a FastQ file + continued learning
Video
Example: www.signalingsystems.ucla.edu/users/Simon/example.fastq

Technical Requirements

  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.
  • If you are bringing your own laptop, please ensure you have Python 3 installed by typing `python3` (or simply `python` on Windows) into your command-line starts a Python session. We will work preferably with Python 3.  If you have any questions please email me or come on the first day up to 30 minutes before the beginning of the workshop.

Instructor

Dr. Alex Brummer is a postdoctoral scholar in Dr. Van Savage’s group through the Depts. of Biomathematics and of Ecology and Evolutionary Biology. Alex is working with the lab software Angicart to digitally reconstruct and analyze vascular tissues from medical images spanning multiple modalities (e.g. MRI, CT, and micro-CT) to search for geometric signatures of disease and recovery. Concurrent with this, Alex is developing and testing new models for asymmetric branching in vascular networks that relate the degree or pattern of asymmetry to biological scaling exponents that encapsulate how metabolic rate, heart rate, and lifespan change with body size across species. Alex earned B.S. degrees in physics and mathematics at Oregon State University, and his M.S. and Ph.D. degrees in physics at the University of Arizona. Email: abrummer@ucla.edu

Video

Reviews

Very clear, perfect pace for beginners, great job, would highly recommend!

Fall 2017 Student

Thank you! It was an excellent course, teaching was perfect.

Fall 2017 Student
I came in with zero experience and I feel much more comfortable with python now.
Spring 2018 Student

Thanks for a great workshop. You provided excellent and useful material for all types of researchers.

Spring 2018 Student

Workshop Details

Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Collaboratory Classroom
Seats Available: 28

Fall 2019 Dates

October 8, 9, and 10, 2019
1:30 PM to 4:30 PM