Introduction to Python for genetics

Course Curriculum

Chapter 1: Introduction to the course

Lecture 1: Course overview/introduction

Lecture 2: About the speed of the lectures

Chapter 2: ####PART 1: BASIC GENETICS ######

Lecture 1: Basic concepts

Lecture 2: The gene-protein flow and building blocks

Lecture 3: Inheritance and recombination

Lecture 4: The transcription process

Lecture 5: The translation process

Lecture 6: Population genetics: the Hardy-Weinberg Theorem

Chapter 3: #####PART 2: PROGRAMMING WITH PYTHON #####

Lecture 1: Introduction to Python

Lecture 2: The importance of Python for biosciences

Lecture 3: The COLAB environment

Chapter 4: Variables and types

Lecture 1: Main variables and types

Lecture 2: Arithmetic operators

Lecture 3: User input

Lecture 4: Exercises

Lecture 5: Solution – Estimating recombination frequency

Lecture 6: Erratum

Lecture 7: Solution – Calculating allele frequencies

Chapter 5: Strings and text manipulation

Lecture 1: Strings – concept and methods

Lecture 2: Exercises

Lecture 3: Solution: finding start and termination codons

Lecture 4: Solution: manipulating a DNA string

Chapter 6: Relational/logical operators and conditional statements

Lecture 1: Relational/logical operators

Lecture 2: Conditional statements

Lecture 3: Nested and complex conditions

Lecture 4: Exercises

Lecture 5: Biomolecule classifier

Lecture 6: Polypetide sequence analysis with string manipulation

Chapter 7: For and while loops

Lecture 1: The for loops

Lecture 2: The "nested" for loops

Lecture 3: The while commands

Lecture 4: Exercises

Lecture 5: Solution – base pairing verification

Lecture 6: Solution – Simulating the transcription process

Lecture 7: Solution – Hamming distance

Chapter 8: Tuples, lists and dictionaries

Lecture 1: Tuples

Lecture 2: Lists

Lecture 3: Dictionaries

Lecture 4: Exercises

Lecture 5: Solution – Transcription process with dictionaries

Lecture 6: Solution – Modelling the translation process

Lecture 7: Solution – challenge 1: RNA splicing

Chapter 9: Functions

Lecture 1: Functions: definition and declaration

Lecture 2: Functions: optional parameters, scope and docstrings

Lecture 3: Exercises

Lecture 4: Solution – A function that extracts the proportion (%) of AT's/CG's

Lecture 5: Solution – function that calculates the recombination frequency

Lecture 6: Solution – Challenge 1: Hardy Weinberg Theorem – interpretation of the results

Chapter 10: Modules

Lecture 1: The math module

Lecture 2: The random module

Lecture 3: The time module

Lecture 4: Exercises

Lecture 5: Solution – generating a random DNA sequence

Lecture 6: Solution – Timing the random sequence generation function

Lecture 7: Solution – Challenge 3: simulating the reproduction of two genotypes

Chapter 11: Handling errors and exceptions in Python

Lecture 1: Types of errors and exceptions in Python

Lecture 2: Try and except

Lecture 3: Exercise

Lecture 4: Solution – treating exceptions in a previous exercise

Chapter 12: Working with text files

Lecture 1: Reading and writing .txt files

Lecture 2: FASTA files

Lecture 3: Exercises

Lecture 4: Reading a Sars-Cov-2 sequence with Python

Lecture 5: Solution: Challenge 3 – part 1

Lecture 6: Solution: Challenge 3 – part 2

Lecture 7: Bonus lecture