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BZ360 Fall 2020 Schedule


Topics Reading/Videos Assignments
Week 1 (8/25, 8/27)
Lecture
(lectures are online)
Introduction to Bioinformatics and Genomics Lecture 1
Lab
(labs are in-person)
Genetic Variation and Sequence alignments
slides
video
Supplement 1: genetic variation Assignment 1
video
Week 2 (9/1, 9/3)
Lecture Next Gen Sequencing (NGS) Technologies
slides
Lecture 2
Supplement 2: Illumina
Supplement 3: PacBio
Supplement 4: Nanopore
Supplement 5: 10xGenomics
Lab Command Line Computing: exercise 1
slides
video
Supplement 6: intro to videos
Supplement 7: central processors
Assignment 2
Week 3 (9/8, 9/10)
Lecture NGS Quality Control
slides
Lecture 3
Supplement 8: FastQC
Lab Command Line Computing: exercise 2
slides
video
Supplement 9: computer memory Assignment 3
Week 4 (9/15, 9/17)
Lecture Read Mapping
slides
Lecture 4
Supplement 10: mapping NGS reads
Lab FastQC and Trimmomatic
slides
video
Supplement 11: hard drives Assignment 4
Remote Login
Week 5 (9/22, 9/24)
Lecture Genomes and Genome Assembly
slides
Lecture 5
Supplement 12: genome sequencing
Supplement 13: the human genome
Supplement 14: genome diversity
Lab Bowtie
slides
video
Assignment 5
Week 6 (9/29, 10/1)
Lecture Introduction to RNA-seq
slides
Lecture 6 Supplement 15: NGS applications
Lab Exam 1 - online
(Thursday 12:30-1:45 pm)
Review session - online
(Tuesday 12:30)
video
study guide
Exam 1
Week 7 (10/6, 10/8)
Lecture RNA-seq: read alignment
slides
Lecture 7
Supplement 16: RNA-seq
Supplement 17: TopHat
Lab RNA-seq: exercise 1
video
Assignment 6
Week 8 (10/13, 10/15)
Lecture RNA-seq: differential gene expression analysis
slides
Lecture 8
Supplement 18: CRISPR
Supplement 19: Doudna, TED Talk
Supplement 20: DGE
Lab RNA-seq: exercise 1 cont.
slides
video
Assignment 7
Week 9 (10/20, 10/22)
Lecture RNA-seq: data visualization
slides
Lecture 9
Supplement 21: IGV
Supplement 22: R
Lab RNA-seq: exercise 1 cont.
video
Assignment 8
Week 10 (10/27, 10/29)
Lecture Introduction to Computer Programming
slides
Lecture 10
Supplement 23: Code Stars
Supplement 24: Programming
Supplement 25: Just for fun
Supplement 26: Python Toolbox
Lab RNA-seq: exercise 1 cont.
slides
video
Assignment 9
Week 11 (11/3, 11/5)
Lecture Python
slides
Lecture 11
Supplement 27: py4e, Ch 1
Lab Bash Scripts and Scratch
slides
video
Assignment 10
mario
pacman
nerf
Week 12 (11/10, 11/12)
Lecture Jupyter Notebook
Lecture 12
Supplement 28: py4e, Ch 2
Lab Print and input functions
slides
video
Install Anaconda
Assignment 11 (pdf)
(web-based)
Problem set 1
(web-based)
Colaboratory
Week 13 (11/17, 11/19)
Lecture Review for exam
Lab Exam 2 - online
(Thursday 12:30-1:45 pm)
Review session - online
(Tuesday 12:30)
video
study guide
Exam 2
Week 14 (11/24, 11/26)
Thanksgiving break
Thanksgiving break
Week 15 (12/1, 12/3)
Lab 1 Conditionals
notebook (pdf)
(web-based)
Lecture 13
Supplement 29: py4e, Ch 3
Lab 2 Functions
notebook (pdf)
(web-based)
Review session
Lecture 14
Supplement 30: py4e, Ch 4
Problem set 2 (key)
(web-based)
Assignment 12
(web-based)
Due 5 pm, Dec 7
Week 16 (12/8, 12/10)
Lab 1 Iteration: for loops
notebook (pdf)
(web-based)
Lecture 15
Supplement 31: py4e, Ch 5
Lab 2 Iteration: while loops
notebook (pdf)
(web-based)
Review session
Lecture 16 Problem set 3 (key)
(web-based)
Assignment 13
(web-based)
Due 5 pm, Dec 14
schedule.txt · Last modified: 2020/12/10 12:30 by dokuroot