SWE4016/DHC3003, Bio-Computing (Introduction to Computational Biology)
2024, 1st Term
Class Hours: Mon/Wed 3:00pm - 4:40pm
Classroom: Mirae-231/234
Professor: Dr. Young-Rae Cho (email: youngcho@yonsei.ac.kr)
Office: Chang-328
TA: Jong-Hoon Park (email: jonghoon_park@yonsei.ac.kr)
Course Web Page: https://ads.yonsei.ac.kr/faculty/biocomputing/
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Description
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Introduction to computational issues on analyzing biological data. The focus of this course is on design and evaluation of algorithms with applications to bioinformatics, and programming to manipulate biological data using Python. Topics include (1) sequence alignment, (2) pattern matching and finding, (3) phylogenetic algorithms, and (4) gene clustering and classification.
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Objectives
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- To understand the basic concepts and techniques on Computational Biology and Bioinformatics.
- To develop computational skills of designing algorithms to analyze biological data.
- To gain experience of programming to manipulate biological data using Python.
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Prerequisites
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- CSE2003/SWE2001, Data Structures
- Python programming skills
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Reference Books
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- An Introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel A. Pevzner, The MIT Press
- Algorithms in Bioinformatics: A Practical Introduction, by W.-K. Sung, CRC Press
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Assignments
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- 9 - 11 programming assignments using Python
- Submission: source codes including comments via LearnUs in class time
- No late-submission accepted
- Grades for students who are absent in practice time are allocated 70% of the average of Assignment scores for the first absence, 30% of the average of Assignment scores for the second absence, and 0 for the third or more absence.
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Exam
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- Midterm: offline exam, closed-book
- Final Exam: offline exam, closed-book
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Grading
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- Programming Assignments: 45%
- Midterm: 20%
- Final Exam: 25%
- Attendance & Participation: 10%
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Policies
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- According to the university policy, absences more than 30% will cause getting an F as the final grade of the course no matter what scores are obtained in exames and assignments. (An official excuse letter will be accepted.)
- Programming assignment is due at 11:59pm on the specified date. Late submission of programming assignments will receive the penalty of 20% per day (including Saturday and Sunday).
- Discussions on the programming assignments are allowed, but all programming assignments must be independent work. Any forms of cheating on the assignments and exam will cause a penalty of getting an F as the final grade of the course according to the university regulation guidelines.
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Topics & Tentative Schedule