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Computers and COVID: An Introduction to Programing and Computational Biology

Department: Bioinformatics and Systems Biology                                  

Instructor: Jennifer L. Havens
Instructor's Email: jhavens@eng.ucsd.edu
Prerequisites: Understanding of Algebra and variables; basic understanding of DNA/genetics and cells will be helpful but all necessary biology background will be covered. 
Section ID: 156934 

Schedule: Class on Mon, Weds, Fri. 1-3PM; Tentative office hours on Tues & Thurs. 2-4PM PST

 
REGISTRATION IS CLOSED FOR SUMMER 2021

Course Description

Computational biology uses computers to address problems that we cannot solve by hand (such as comparing 400,000+ 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. We will also have discussions about a selection of scientists: who they are and what they have contributed to the field.

Course Goals / Learning Objectives

By the end of this course, students will be able to:

  • Design and implement python programs when presented with simple problems
  • Use existing python tools to address more complex problems
  • Summarize central dogma of genetics
  • Model genetic evolution
  • Intuitively understand the theory underlying statistical randomization test
  • Breakdown challenges into smaller problems
  • Apply their skills and knowledge to topical problems: Modeling how SARS-CoV2 and other viruses can infect people though their cells, and spread in populations

Course Topics

Tentative 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.