Genome 559

Course description

Rudiments of statistical and computational genomics. Emphasis on basic probability and statistics, introduction to computer programming and relevant web databases. This course is intended to introduce students with non-computer science backgrounds to the major concepts of programming and statistics.

Instructional staff

Meeting times and locations

Prerequisites

 

Substantial background in molecular and cellular biology, genetics, biochemistry, or related disciplines.

Course materials

 

Readings for the Python parts of the class will be assigned from the free online textbook Think Python.

Course requirements

 

  • The course involves hands-on programming during class time, so students should bring a laptop to class.

  • Late homework will be accepted, but penalized. Specifically, each assignment is worth 100 points, from which 10 points will be deducted for each day (or fraction thereof) that you turn it in late. The maximum deduction for being late is 60 points (even if you are more than 6 days late).

  • You are welcome to talk to classmates about principles for solving problems, but please do not share code or solve specific problems together. The problem solving is where you will learn the most for this class, especially the programming.

Examinations

 

There will be an in-class final exam on the last day of class.

Course grade

 

Grades will come 80% from problem sets and 20% from one final exam. There will be no mid-term exam. The final course grade is computed using the procedure described here.

Home page

 

Class schedule

Thurs

Feb 20

Modules

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Tues

Feb 25

Clustering,

hierarchical clustering

More on functions, 

sorting

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Thurs

Feb 27

K-means clustering

Classes and objects 1

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Tues

Mar 3

Biological networks and 

Dijkstra's algorithm

Classes and objects 2

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Thurs

Mar 5

Biological networks and

network motifs

Classes and objects 3

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Tues

Mar 10

Regular expressions

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Thurs

Mar 12

User experience

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Mon

Mar 16

Final Exam

10:30 a.m. – 12:20 p.m.

Foege S-040

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Date
Lecture Topic
Programming Topic
Reading
Homework
Assigned
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