Week Name Description
File Syllabus

Syllabus

File Calendar

Calendar

URL Final Project Groups

Final Project Groups

24 January - 30 January File M01 Handout 00: Overview

Introductions and course logistics

File M01 Notes: Descriptive statistics

Data visualization, summary statistics, parametric and nonparametric summaries, sample and vector comparisons

File M01 Presentation: Introduction

Data visualization

File M01 Handout 01: Probability

Optional reading, notes from another course introducing probability theory and combinatorics.

File Reading: Qin Nature 2010

Qin Nature 2010

File Problems 00: Pre-test

Problems 00: Pre-test

File Problems 01: Quantitative methods

Data visualization, descriptive statistics, simple parametric tests, conditional probability.

File W01 Notes: Inference and hypothesis testing

Basic probability theory, hypothesis testing, parametric and nonparametric tests, p-values, multiple hypothesis testing, performance evaluation.

URL Reading: Understanding ANOVA Visually
File R01 Handout 02: Installing Python

R01 Handout 02: Installing Python

File Lab 01: Python Setup
Instructions for installing Python, jEdit, and IPython, along with a short introduction to the command line.
File Activity 01: Multiple sample hypothesis tests (download)

Samples, two-way parametric tests (t-tests), two-way nonparametric tests (Mann-Whitney), parametric ANOVA, and nonparametric Kruskal-Wallis

URL Activity 01: Multiple sample hypothesis tests (view)

Samples, two-way parametric tests (t-tests), two-way nonparametric tests (Mann-Whitney), parametric ANOVA, and nonparametric Kruskal-Wallis

31 January - 6 February File M02 Notes: Introduction to Python

M02 Notes: Introduction to Python

File M02 Notes: Introduction to Python (extended)
File M02 Handout 03: Submitting Python problems

M02 Handout 03: Submitting Python problems

Page Reading: Practical Computing
File Reading: Dudley PLoS CB 2009
File Problems 02: Introduction to Python

Problems 02: Introduction to Python

File W02 Notes: Python primitives and functions
File W02 Notes: Python primitives

W02 Notes: Python primitives

File W02 Notes: Functions

W02 Notes: Functions

File Activity 02: Performance evaluation (download)

Pairwise similarity scores, performance evaluations, evaluation measures, and precision/recall and ROC plots.

URL Activity 02: Performance evaluation (view)

Pairwise similarity scores, performance evaluations, evaluation measures, and precision/recall and ROC plots.

File Lab 02: Python Practice

The second lab, which reviews class concepts has some basic Python exercises.

File Lab 02: Python Practice (script)

A toy Python script for practicing.

File Lab 02: Python Practice (key)

The key for the questions asked about the python practice in lab.

File Lab 02: Python Practice (script key)

Key for the script they will generate in lab.

File Lab 02: Shortcuts Terminal
File Lab 02: problem02 (example)

Example of the python script that you should submit for your homework.

7 February - 13 February File M03 Notes: References and Modules

W03 Notes: References and Modules

File M03 Notes: Supplemental Examples

M03 Notes: Supplemental Examples

File M03 Notes: References

W03 Notes: References

Page Reading: Practical Computing
File Reading: Cock Bioinformatics 2009
File Problems 03: Reading and Writing Data

Problems 03: Reading and Writing Data

File W03 Notes: I/O (abbreviated)

W03 Notes: I/O (abbreviated)

File W03 Handout: I/O (extra details)

W03 Handout: I/O (extra details)

File W03 Supplemental Examples

W03 Supplemental Examples

Folder W03 Data Files

W03 Data Files

File Activity 03: Modules and I/O (download)

Writing bioinformatics functions, importing and using modules, input/output streams and file handling.

URL Activity 03: Modules and I/O (view)

Writing bioinformatics functions, importing and using modules, input/output streams and file handling.

File Lab 3

Lab 3 materials

File Lab 3 Solutions

Lab 3 Solutions

14 February - 20 February File Problems 04: Regular Expressions and Data Stores

Problems 04: Regular Expressions and Data Stores

File e.coli.pos
File e.coli.genome
File Reading: Jensen Nature 2006
File W04 Notes: Regular Expressions

W04 Notes: Regular Expressions

Page Reading: Regular Expressions

Reading: Regular Expressions

Page Reading: Practical Computing
Folder Lab 04 - Regular Expressions

Lab 04 - Regular Expressions

21 February - 27 February File M05 Notes: Data handling and command environments

M05 Notes: Data handling and command environments

File Reading: Noble PLoS CB 2009
Page Reading: Practical Computing
Page Reading: Testing, arguments, and command line tools

Reading: Testing, arguments, and command line tools

File W05 Notes: Computational experiments

W05 Notes: Computational experiments

File Activity 04: Reproducible research

Activity 04: Reproducible research

File Activity 04: Reproducible research (data)
Folder Lab 5: doctests and debugging

Doctests and debugging

28 February - 5 March File M06: Genomes and sequence alignment

M06: Genomes and sequence alignment

File M06 Presentation: Genomic data resources

M06 Presentation: Genomic data resources

File M06: Genome sequences supplementary material

M06: Additional slides for genomes, sequence alignment, and sources of genomic data

Page Reading: Bioinformatics and Functional Genomics
File Reading: Sela PNAS 2008
File Problems 05: Genomes and Sequencing

Problems 05: Genomes and Sequencing

File Problems 05: Genomes and Sequencing (data)
File Problems 05: Genomes and Sequencing (MacOS samtools)
File Problems 05: Genomes and Sequencing (32-bit MacOS samtools)

Problems 05: Genomes and Sequencing (32-bit MacOS samtools)

File W06 Notes: High-throughput sequencing

W06 Notes: High-throughput sequencing

File W06 Presentation: High-throughput sequencing

W06 Presentation: High-throughput sequencing

File W06 Presentation: Illumina sequencing
File W06 Presentation: PacBio sequencing

W06 Presentation: PacBio sequencing

Page Reading: Bioinformatics and Functional Genomics
Folder Lab 06

Python practice problems.

Folder Python Cheat Sheet
I found 3 different Python cheat sheets that you may find useful while doing your homework.
6 March - 12 March File M07 Presentation: Sequence analysis

M07 Presentation: Sequence analysis

Page Reading: Bioinformatics and Functional Genomics
File Reading: Venter Science 2004
File Problems 06: Metagenomics

Problems 06: Metagenomics

File Problems 06: Metagenomics (data)
File Problems 06: Metagenomics (32-bit MacOS mothur)

Problems 06: Metagenomics (32-bit MacOS mothur)

File W07 Presentation: Metagenomics

W07 Presentation: Metagenomics

File Lab 07

Lab 07

20 March - 26 March File M08: Gene Expression Data

M08: Gene Expression Data

Page Reading: Bioinformatics and Functional Genomics

Pevsner, Third edition

File Reading: Hughes 2000 Cell
File Problems 07: Gene Expression

Problems 07: Gene Expression

File Problems 07: Gene Expression (data)
File W08: Gene Expression Analysis

 W08: Gene Expression Analysis

File Lab 08

Spring 2016

27 March - 2 April File M09 Presentation: Transcriptional Regulation

M09 Presentation: Transcriptional Regulation

Page Reading: Regulation and Epigenetics

Pevsner, third edition

File Reading: ENCODE PLoS Biology 2011
File Problems 08: Transcriptional Regulation

Problems 08: Transcriptional Regulation

File W09 Presentation: Comparative Genomics

W09 Presentation: Comparative Genomics

File W09 Notes: Journal club and final projects

W09 Notes: Journal club and final projects

Folder W09: Comparative Genomics Activity

W09: Comparative Genomics Activity

File Python Exercises

Rosalind Project python problems

3 April - 9 April File M10 Presentation: Epigenetics

M10 Presentation: Epigenetics

File Reading: Workman Science 2006

Reading: Workman Science 2006

File Problems 09: Review

Problems 09: Review

File W10 Presentation: Biological Network Analysis

W10 Presentation: Biological Network Analysis

10 April - 16 April File M11 Presentation 1: Proteomics

M11 Presentation 1: Proteomics

File M11 Presentation 2: PPIs

M11 Presentation 2: PPIs

File Reading: Costanzo Science 2010
Page Reading: Proteins and PPIs

Pevsner, third edition

File Problems 10: Biological Network Analysis

Problems 10: Biological Network Analysis

17 April - 23 April Folder Journal Articles for Monday 4/18/2016

Journal Articles for Monday 4/18/2016 

Folder Journal Articles for Wednesday 4/20/2016

Journal Articles for Wednesday 4/20/2016

Folder Journal Articles for Monday 4/25/2016

Journal Articles for Monday 4/25/2016