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Computational Systems Biology |
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Course Information
Location/Time: PSB 305, Tues/Thurs: 2-3:45 pm
Information and Handouts
Course Description & Objectives
- Manipulation of large files and organizing data flow in a UNIX-like operating system
- Implementing and evaluating unsupervised, supervised, and semi-supervised algorithms taught in class.
- Reviewing a sub-field related to Systems Biology.
- Participation in a team project with the aim of integrating two or more sources of data to make inferences about gene function.
- Presenting the results of the team project in a 5pg Methods paper and a 10 minute presentation describing the method.
To connect with current research in this emmerging field, the course includes a journal club component.
Prerequisites
Grading
Grades are based on three homework assignments (30%), a mini-review (10%), a mid-term exam (20%), a final exam (20%), and a final programming project (20%). Note that the homework assignments will require some programming.
Mini-reviews
You'll be responsible for hosting a 20-minute presentation of a research topic. You will be evaluated on your ability to overview a sub-field, select (at least two) seminal papers in the area, describe (at least two) non-trivial mathematical or computational formulations that had key impacts in the area, answer questions, promote discussion, and your overall organization. You may work with a partner. You will be required to turn in any visual aids you can (e.g. powerpoint slides). If you give a "chalk-talk," you will need to provide handouts that include an outline and any equations you present. Please see the topics page for a list of suggested topics and sub-topics.
Final Programming Projects
You may work in teams of 1-3 people on the final programming project. You will compete in a gene function prediction challenge. Each team will create a program that assigns gene function categories to genes with associated molecular fingerprints. Programming projects will be graded on a ~10 page writeup of the methods, if the code executes properly and performs competitively, and a 10 minute oral presentation that describes the team's unique approach.
Working in Groups
You may work with a partner on homework assignments and your hosted journal club. Please include, with your name, the name of your teammate on all documents that you turn in. (Note:
Late Policy
Each student can use a total of 7 late days on all homework assignments. A maximum of 3 late days can be used on any one assignment. No late days can be used for the mid-term, final, topical presentations, or final programming projects.
Extra Credit
Eextra credit is available for scribing lectures. You can earn as much as 5% extra credit. The amount depends on the quality of the scribed notes. Notes should be written in LaTex, contain relevant figures from the lecture, and follow the instructions on the Scribing Instructions page
Communication |
We strongly encourage students to come to office hours.
Please do not e-mail the instructors with grading questions. If you want us to explain why we took points off, you can talk to us after class or during office hours. If you want a re-grade, please write an explanation and hand the homework and the explanation to one of the instructors during office hours or after class.
Textbook Information |
There is one required textbook for the course:
"Systems Biology in Practice. Klipp, Herwig, Kowald, Wierling, Lehrach.
- It's fairly expensive if purchased from the bookstore (~$180 after taxes).
- ValoreBooks has it for $83 (incl S+H) [url].
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