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

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

Dr. Renaud Dessalles is a Post-Doctoral researcher at the laboratory of Biomathematics currently working on the modeling of the immune responses to antigens. His main interested consist in mathematical and computational modeling applied to biology, using mainly (but not exclusively) stochastic models. During his PhD in applied mathematics at INRA and INRIA (France), he worked on the stochastic modeling of protein production inside bacteria. Renaud’s main skills consist of the analysis of stochastic and deterministic models and the use of several computational language (Python, C++, Matlab, Julia) for simulations.

Email: dessalles@ucla.edu

Reviews

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

Anonymous

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

Anonymous

Workshop Details

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

Winter Dates

Jan. 9 – 11, 1pm – 4pm