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Computers and COVID: An introduction to programing and computational biology

Department: Bioinformatics and Systems Biology

Instructor: Jennifer Havens
Instructor Emails:
Prerequisites: Understanding of algebra and variables
Dates: July 11 - July 29, 2022
Schedule: 9am - 4pm (Lunch from 11:30am - 1:30pm)
Location: UC San Diego Extended Studies, 9600 N. Torrey Pines Road, La Jolla, CA 92037
Room: Please refer to Instructor's Canvas page and email correspondance for information 

Course Description

Computational biology, uses computers to address problems that we cannot solve by hand (such as comparing 4million+ COVID genomes). In this course students 1) will learn the basics of programming in the coding language python 2) learn about selected molecular biology topics 3) write programs to analyze data to understand what is happening biologically. The course will be structured with lectures and class worktime. There will be coding problems, conceptual questions, and some reading.

Course Goals / Learning Objective

By the end of course students will be able to:

Summarize the so called ‘central dogma of genetics’ (DNA -> RNA -> protein)
Given a situation (an example case), explain how to set up statistical randomization test, and explain meaning of output (p-value)

Design and implement python programs when presented with simple problems
Use existing python tools to address more complex problems
Model genetic evolution using computer simulations

Transferable / soft skills
Formulate a breakdown of a larger challenge into smaller problems

Course Topics

  • Coding in python
    • Variables and data structures: string, list, float, int, dictionary
    • Flow instructions: if/else logic, functions
    • Basic algorithms: loops, recursion
    • Using packages
  • Math/statistics
    • Randomization test
    • P value
  • Biology
    • Immune system
    • Central dogma of molecular biology
    • Mutations in DNA and selection
  • Applications
    • Virus spreading in tissue
    • DNA sequence alignment
    • Phylogenetic tree building
    • Reconstructing geographic spread of epidemic (phylogeography)


*Courses vary by experience and exposure to content. Instructors have the ability to change content and pace to serve the needs of students. Courses have been modified for online teaching.