Workshop Description (Introductory Course)

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:

Workshop Materials

Slides for day 1 –Click 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

Slides for day 2 – Click 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

Slides for day 3 – Click 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.
  • Prior to arriving at the workshop, please download the Anaconda Distribution at https://www.anaconda.com/distribution/.  Be sure that you download the Python 3.7 version. With this download you will automatically receive Spyder and Juptyer, the two software packages that will be used during the workshop.
  • Workshop time is limited, so please ensure prior to arriving at the workshop that you have successfully installed all needed software on your computer (Anaconda, Spyder and Jupyter) and that it all runs correctly.  Helpful instructions for these checks can be found at the “Getting Started” section of the Anaconda User Guide website https://docs.anaconda.com/anaconda/user-guide/getting-started/.  Any issues are most likely due to incorrect installation, which is addressed in the FAQ page at https://docs.anaconda.com/anaconda/user-guide/faq/.

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 2019 Student

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

Fall 2019 Student
I came in with zero experience and I feel much more comfortable with python now.
Spring 2019 Student

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

Spring 2019 Student

Workshop Details

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

Spring 2020 Dates

March 31, April 1, and 2
1:30 PM to 4:30 PM

REGISTRATION IS CLOSED!