Week Name Description
File Syllabus

Syllabus

File Calendar

Calendar

URL Bioinformatics and Functional Genomics

Bioinformatics and Functional Genomics

27 January - 2 February 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: Arumugam Nature 2011
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

3 February - 9 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.

10 February - 16 February File W03 Notes: References and Modules
File W03 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 Lab 3

Lab 3 materials

File Lab 3 Solutions

Lab 3 Solutions

17 February - 23 February File W04 Notes: I/O (abbreviated)

W03 Notes: I/O (abbreviated)

File W04 Handout 04: I/O
File Activity 04: Modules and I/O (download)

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

URL Activity 04: Modules and I/O (view)

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

File Reading: Jensen Nature 2006
Folder Lab 04: File I/O

Lab 04: File I/O

24 February - 2 March File M05 Notes: Regular Expressions

M05 Notes: Regular Expressions

URL M05 Regular Expressions: Script

M05 Regular Expressions: Script

URL M05 Regular Expressions: Sample Text

Sample Text

Page Reading: Practical Computing
Page Reading: Regular Expressions

Reading: Regular Expressions

File Reading: Noble PLoS CB 2009
File Problems 04: Regular Expressions and Data Stores

Problems 04: Regular Expressions and Data Stores

File e.coli.pos
File e.coli.genome
File W05 Notes: Data handling and command environments

W05 Notes: Data handling and command environments

Page Reading: Practical Computing
Page Reading: Testing, arguments, and command line tools

Reading: Testing, arguments, and command line tools

Folder Lab 05 - Regular Expressions

Lab 05 - Regular Expressions

3 March - 9 March File M06: Genomes and sequence alignment

M06: Genomes and sequence alignment

File M06 Presentation: Genomic data resources

M06 Presentation: Genomic data resources

File Sequences for practice

Sequences for practice

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 Presentation: High-throughput sequencing

W06 Presentation: High-throughput sequencing

File W06 Presentation: 454 sequencing
File W06 Presentation: Illumina sequencing
File W06 Presentation: PacBio sequencing

W06 Presentation: PacBio sequencing

File W06 Presentation: Ion Torrent sequencing

W06 Presentation: Ion Torrent sequencing

Page Reading: Bioinformatics and Functional Genomics
Folder B.longum from GenBank FTP
Use these files for Problem 4 if you can't connect to GenBank FTP yourself.
File Lab 06 Key

Lab 06 Key

File Lab 6

  

10 March - 16 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

24 March - 30 March File M08: Gene Expression Data

M08: Gene Expression Data

Page Reading: Bioinformatics and Functional Genomics
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

Lab 08

31 March - 6 April File M09 Presentation: Transcriptional Regulation

M09 Presentation: Transcriptional Regulation

Page Reading: Regulation and Epigenetics
File Reading: ENCODE PLoS Biology 2011
File Problems 08: Transcriptional Regulation

Problems 08: Transcriptional Regulation

Folder W09: Comparative Genomics

W09: Comparative Genomics

File Lab 09

Lab 09

7 April - 13 April File M10 Notes: Journal club and final projects

M10 Notes: Journal club and final projects

File Reading: Workman Science 2006

Reading: Workman Science 2006

File Problems 09: Comparative Genomics

Problems 09: Comparative Genomics

File Problems 09: Comparative Genomics (data)
Folder M10: Experimental Design

Experimental Design

Folder W11:Networks

W11:Networks

Folder Lab 10

Lab 10

14 April - 20 April File M11 Presentation: Proteomics

M11 Presentation: Proteomics

File Reading: Costanzo Science 2010
Page Reading: Proteins and PPIs
File Problems 10: Biological Network Analysis

Problems 10: Biological Network Analysis

Folder Problems 10 Data

Problems 10 Data

File W11 Presentation: Genetic Interactions

W11 Presentation: Genetic Interactions

Folder Lab 11

Lab 11