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

Workshop Materials

The classroom is equipped with 10 iMacs. If you would like to reserve an iMac for use in the collaboratory, please indicate so on the registration page. If you are brining your own laptop, please  ensure you have Python installed and that typing Python into your command-line starts a Python session. Both Python version 2 and 3 will be fine. If you have any questions please email me or come by on the Monday before the workshop to my office in room 570 Boyer Hall (down the hall from the Collaboratory classroom).

Instructor

Simon Mitchell is a postdoc in computational systems biology working with Professor Alexander Hoffmann. He is working in constructing mathematical simulations of immune systems and cancer. Prior to joining UCLA, his undergraduate studies in computer science and math led him to a PhD investigating the computational modeling of human iron metabolism at the University of Manchester. Dr. Mitchell’s general interests lie in programming, computational biology, mathematical modeling, sensitivity analyses and translational research.

Email: Simon.Mitchell@ucla.edu

Workshop Details

Prerequisites: None
Length: 3 days, 2hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Winter/Spring Dates

5/23/17 – 5/25/17, 10AM