Bioinformatics Education - Bionformatics course on Coursera

 At 2013-09-26 12:07:12 AM  |   247

About the Course

The sequencing of the human genome a decade ago fueled a computational revolution in biology, which has arguably been an impetus for more new algorithms than any other fundamental realm of science.  The newly formed links between computer science and biology affect the way we teach computational ideas to biologists, as well as how applied algorithms are taught to computer scientists. 

Genome sequencing is just one of hundreds of biological problems that have become inextricable from the computational methods required to solve them. In this course, we will take a look at some of the algorithmic ideas that are fundamental to an understanding of modern biology.  Computational concepts like dynamic programming and graph theory will help us explore algorithms applied to a wide range of biological topics, from finding regulatory motifs to reconstructing the tree of life.  Throughout the process, we will apply real bioinformatics algorithms to real genetic data.

In order to streamline homework assignments and solidify the material covered in the course, we will employ Rosalind, a fun new resource for learning bioinformatics that was founded by the instructors.  We hope that Rosalind will show you how fun solving problems in bioinformatics can be.

Course Syllabus

Note: the syllabus may undergo revisions throughout the course. 

Each homework will contain 5-10 programming assignments.

The course will consist of the following seven primary topics:

  • Finding the Replication Origin in Bacterial Genomes
  • Sequencing Antibiotics
  • Genome Assembly
  • Genome Rearrangements
  • Finding Regulatory Motifs
  • Sequence Alignment
  • Short Read Mapping

Recommended Background

You should know the basics of programming in any language that you choose.  If you don’t know how to program, working introductory problems on Rosalind will help introduce you to Python (approximately 10 hours of work).

Suggested Readings

 Bioinformatics Algorithms: An Active-Learning Approach, by Compeau & Pevzner. 

Course Format

The class will offer two ways of learning the material.  The primary content for the course is the textbook Bioinformatics Algorithms: An Active-Learning Approach, by Compeau & Pevzner.  This textbook (to become available in October 2013) is a streamlined interactive textbook with homework problems and quiz exercises integrated directly into the text.

The course will also feature a collection of video lectures that can be used either as a supplement to the text or as standalone lectures for students who wish to understand the key ideas of the course.

FAQ

  • Will I get a statement of accomplishment after completing this class?

Yes. Students who successfully complete the class will receive a statement of accomplishment signed by the instructor.

 

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