User Tools
Sidebar
schedule
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: 2021/06/01 15:05 (external edit)
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
