- Instructor: Vikas Bansal (vibansal at ucsd.edu)
- Office hours: Monday, 1-2 pm, BRF-2 2119
- Primary: Peter Edge (Office hours: Friday, 2-3 pm, CSE 4256)
- Additional: Mehrdad Bakhtiari (Office hours: Thursday 4-5 pm, CSE 4250)
- Additional: Lihui (Luna) Lu (Office hours: Wednesday 12:00pm-2:00pm, CSE B260A)
- Lectures (Tuesday/Thursday 2-3:20 pm) in HSS 1128A
- Discussion section: Friday, 1:00-1:50 pm in WLH 2207 by Peter Edge
- midterm (in class, 05/10/2018): Syllabus includes everything till 5/3/2018 lecture. Please bring a calculator & your ID. You can bring a one-page hand-written sheet of notes
- final (06/09/2018, 8-11 am), CENTR 109. Please bring a calculator & your ID. You can bring a one-page hand-written sheet of notes
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This course will provide an introduction to Biological data analysis including the underlying methods for querying Biological databases. Not much biology background is needed but familiarity with programming, algorithms and data structures is needed. Another section for this course is being taught concurrently by Professor Vineet Bafna and the two sections will cover the same material.
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There is no required textbook for this course, lecture slides will be provided on the course webpage but are not a substitute for lecture notes. References for each lecture and recommended reading will be provided as needed. For Biology, the classic reference Molecular Biology of the Cell is available online.
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Outline of the syllabus for the course is available here
- 50% for assignments (5 in total)
- Students can do a project instead of the last two assignments. Projects can be done in teams of 2-3. If you decide to do a project, you cannot change your decision later on.
- 20% for midterm
- 30% for final
- Lecture Slides
- Piazza Discussion Board (to ask questions about or discuss course material/logistics)
- Gradescope (to submit homework assignments, code MKYE7Z for signup)
- Academic Integrity
- Submit the code and the output for the assignment via Gradescope.
- Late assignment policy: 10% off for each day after the submission deadline.
- No submission accepted 3 days beyond due date.
- Regrade requests must be made on Gradescope within 7 days after graded assignments are returned. No regrade request will be accepted subsequently.
| Assignment | Due Date | Data & Resources |
|---|---|---|
| A1 | 04/10/2018 (midnight) | Datafile |
| A2 | 04/25/2018 (midnight) | problem 1 sequences, problem 4 sequences (right click to download) |
| A3 | 05/14/2018 (midnight) | README DNA database query keywords 1 query keywords 2 |
| Projects | 06/11/2018 | |
| A4 | 5/29/2018 (midnight) | chrA.fasta chrA.islands chrB.fasta |
| A5 | 06/11/2018 (midnight) | expression.txt |
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