Modern biological techniques are generating a variety of large-scale data, and require sophisticated algorithms for their analysis. Tasks include assembling the genomic sequence, predicting the protein-coding regions, their function and the manner in which they are regulated. The course will provide a broad overview of the computational techniques currently used in bioinformatics. Students completing the course will be able to analyze a variety of biological data, a skill they will develop through the hands-on lab component, which will consist of algorithm implementation and biological case studies using those algorithms. Computational techniques covered in the course include dynamic programming for sequence alignment, hidden Markov models for gene finding, and graph algorithms for sequence assembly and motif finding.
CS320 is the only prerequisite for this course.
Neil C. Jones and Pavel A. Pevzner. An introduction to bioinformatics algorithms. MIT Press, 2004.
Here are the formally graded elements of the course and associated weighting:
|Assignments (5)||50 %|
|Final Exam||30 %|
Midterm and Final: Make-up exams are only given in extraordinary circumstances (e.g., illness, family emergency). Students must consult with the instructor as soon as possible. Course examination dates are listed in the syllabus; be aware of them and plan accordingly.
Projects: Unless otherwise specified, programming assignments are to be submitted electronically. Specifics will be included in each assignment. Always check the assignment page for due dates. Late assignments submitted within 48 hours of the time required will receive a 10% late penalty. Electronic submission is closed 48 hours after assignments are due; students not having submitted programs receive an automatic zero on the assignment.
|Midterm||Oct 17, 2019|
|W day||Oct 21, 2019|
|Final||Dec 18, 2019|
The midterms and final will be held in the same classroom as regular lectures. While no change to the midterm dates is anticipated, the instructor reserves the right to change these dates with a week's notice.
All students are expected to conduct themselves professionally. We (the instructors and GTAs) assume you are familiar with the policies in the student information sheet for the department. Additionally, you are computing professionals, albeit perhaps just starting. You should be familiar with the code of conduct for the primary professional society, ACM. You can read the ACM Code of Conduct HERE.
We work to maintain an environment supportive of learning in the classroom and laboratory. Towards that end, we require that you be courteous to and respectful of your fellow participants (i.e., classmates, instructors, GTAs and any tutors). In particular: