Syllabus

Basic concepts and tools for storing, retrieving, and analyzing biological data sets: relational databases, on-line databases, structured query language, scripting for automating interaction with databases and data analysis, digital images and movies, advanced topics.

The evaluation will consist of 4 assignments, 1 mid-term and 1 final exam.

Topics & Key words

Course informations

Instructor: Jérôme Waldispühl

Lectures: Monday/Wednesday/Friday 12:35am - 13:25am.
Monday and Friday classes are in Trottier 3120 and Wednesday lecture in Trottier 060.

Office hours: By appointement.

Assignments and homeworks

Assignment 1 (Due February 6, 2013): [Questions] [Solutions]

Assignment 2 (Due March 1, 2013): [Questions] [Solutions]

Assignment 3 (Due April 5, 2013): [Questions] [Solutions]

Assignment 4 (Due April 16, 2013): [Questions]

Schedule and Material

Lecture 1 (January 8, 2013):
Basics of UNIX commands (1) [Slides]

Lecture 2 (January 10, 2013):
Basics of UNIX commands (2) [Slides] [Supplementary material]

Lecture 3 (January 14, 2013):
Python [Slides]

Lecture 4 (January 16, 2013):
Fundamentals of Python [Slides]

Lecture 5 (January 18, 2013):
For loops, If-Then-Else, Strings [Slides]

Lecture 6 (January 21, 2013):
Regular expressions in Python [Slides]

Lecture 7 (January 23, 2013):
Regular expressions and PROSITE patterns [Slides].

Lecture 8 (January 28, 2013):
Dictionaries [Lecture Material].

Lecture 9 (January 30, 2013):
Plotting data using Matplotlib [Slides].

Lecture 10 (January 30, 2013):
Analysis of mRNA sequence with Matplotlib (1). [Slides] [Solution]

Lecture 11 (February 4, 2013):
Analysis of mRNA sequence with Matplotlib (2). [Slides] [Solution] [Solution 2]

Lecture 12 (February 6, 2013):
Heatmaps and bar charts with Matplotlib. [Slides]

Lecture 13 (February 8, 2013):
Gene Expression Data Visualization. [Slides] [Solution] [datafile]

Lecture 14 (February 10, 2013):
Gene Expression Data Visualization.

Lecture 15 (February 13, 2013):
BioPython. [Slides]

Lecture 16 (February 15, 2013):
Manipulating Rfam data with BioPython. [Slides]

Lecture 17 (February 18, 2013):
Manipulating GenBank data with BioPython. [Slides] [Solution]

Lecture 18 (February 20, 2013):
3D molecular structures with BioPython. [Slides]

Lecture 19 (February 22, 2013):
3D structure analysis using BioPython. [Slides] [Solution] [datafile]

Lecture 20 (February 25, 2013):
3D structure analysis using BioPython. [Solution] [datafile]

Lecture 21 (February 27, 2013):
Review.

Lecture 22 (March 1, 2013):
Mid-term Practice. [Questions] [Solutions]

Lecture 23: (March 13, 2013)
EMBOSS software suite.

Lecture 24: (March 15, 2013)
Using EMBOSS. [Questions] [Solutions]

Lecture 25: (March 18, 2013)
Using EMBOSS part 2 [Questions]

Lecture 26: (March 20, 2013)
Visualizing alignements and multiple sequence alignments.

Lecture 27: (March 22, 2013)
Multiple sequence alignment formats. [Solution]

Lecture 28: (March 25, 2013)
BLAST [Questions]

Lecture 28: (March 27, 2013)
RNA secondary structure [Slides]

Lecture 29: (April 3, 2013)
Subprocess module.

Lecture 30: (April 10, 2013)
Review and subprocess module practice. [Material]

Credits

Thanks to Derek Ruths for sharing his material for this class.