CS 341: Syllabus

Syllabus for Fall 2012

Course Outline

This course is an introduction to the field of molecular systems biology, which aims to understand the mechanisms underlying complex biological processes. Key to this endeavor is the process of formulating and analyzing mathematical models. In this course, we will learn how to relate mechanistic insights gleaned from data to cartoon drawings of the system, then how to translate the cartoon drawing into mathematical expressions, next how to use optimization techniques to fit any unknown parameters, and finally how to analyze models by simulating biological experiments and assessing sensitivity to perturbation.

Topics

Grading

The course grade will be determined as follows:

Homework Assignments 20%
Projects 60%
Class Participation 5%
Final Exam 15%

Homework and Projects

There are two types of work you need to do outside of class: (1) homework assignments which help you learn new material (by reading or trying out some new code), and (2) projects, which give you the opportunity to study a topic in depth. At no class meeting will you have a both a homework assignment and a project due, but on most days there will be both a project and a homework due at some point in the future. Please plan accordingly. You will need to balance both types of work for this course. In general, homework assignments are meant to give you additional practice with coding and to learn new material. Grading for the homework assignments will be essentially boolean. As long as you turn in a complete set of answers and demonstrate (with the quality of the answer) that you put your best effort into them, you will receive full credit. Late or incomplete homeworks will have points deducted. Projects are meant to be more polished and will be graded with greater attention to detail (see below).

Homework Assignments

For most class meetings, there will be an assignment to help you to prepare for the meeting. Sometimes, this will mean reading one or more journal articles and answering questions about them. Other times, it will mean writing some Matlab code. A note about the readings: Instead of using a textbook for this course, we are going straight to the source, and will be reading journal articles. To help you make the most this experience, all readings will be accompanied by a set of questions. The questions are designed to help you get the most out of the paper.

Projects

There will be one project for each topic in covered in the course. This means there will be approximately 5 projects, all of which give you the opportunity to explore that topic in depth. For each project, you will implement Matlab programs, analyze results, and write a short document summarizing and analyzing your methods and results. A set of questions will provide the framework for your code-writing and analysis. Because I want you to have the chance to engage deeply and to have some intellectual autonomy, these questions are intentionally open-ended and there will not be a detailed set of instructions.

The write-ups should be neat and thorough, yet succinct. Answering all of the questions adequately will earn you a B+. To earn an A- or A, you must be particularly convincing and thorough when you answer the "why?" or "how?" or "what if?" questions. This does not mean that I want you to turn in reams of paper. It means that you should include carefully chosen additional examples or evidence to back up your point. The questions I will be asking myself when I am grading are, for example: Does this make sense? Does she make it clear why she came to her conclusions? Is he being precise? Does he include the appropriate mathematics when they are called for? Is her intuition grounded in a solid understanding of the material? Projects are graded on a 30 point scale. Here is a rough guide to grading:

Answers are well-written, show depth of understanding, and include appropriate figures. Additional code or simulations are used to back up points. 30
Answers are well-written, show some depth of understanding, and include appropriate figures. There may be a small amount of additional code or simulations used to back up points. 28
Answers are well-written, show some depth of understanding, and include appropriate figures. No extra work was done. 26
Answers are understandable, show some understanding, and include appropriate figures. No extra work was done. 25

Class Participation

You are expected to attend every class. Some class meetings will involve hands-on lessons difficult to make up. Other class meetings will involve discussion, which is a vital part of the learning experience and we cannot have good discussion without you! Class participation is so important that 5% of your grade depends upon your participation.

Academic Honesty

Honesty is at the heart of the academic enterprise. I do not expect to encounter any dishonesty among mature computer science students, but if the unexpected happens, I will not hesitate to follow the procedures in the Colby College catalogue. If you have any questions, please ask me!

Office Hours

Please visit me in my office! During office hours, I will of course be available. Outside of office ours, I will often be in my office with the door open. Please come in! If you want to be sure I will be there, just ask me in person or send me an email. I will do my best to be there.