### Syllabus for Fall 2009

### 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

- Formulating Models using Standard Kinetics (what math to use)
- Simulation Techniques (how to solve ODE's with a computer)
- Parameter-Fitting through Optimization (finding parameter values that minimize our error)
- Sensitivity Analysis (how does the model react to changes in paramaters?)
- Modeling Noisy Biological Systems (if we incorporate the noise seen in biological systems, how do our simulations change?)

### Grading

The course grade will be determined as follows:

Reading Assignments | 15% |

Projects | 55% |

Class Participation | 5% |

Midterm Exam | 10% |

Final Exam | 15% |

The minimum course grade you will receive is based on your total point score (between 0 and 100%) and is shown below. Grades may be raised and plusses or minuses added at the instructor's discretion.

A | 90-100% |

B | 80-90% |

C | 70-80% |

D | 60-70% |

F | below 60% |

### Reading Assignments

We will be reading journal articles. To help you make the most this experience, all readings will be accompanied by a set of questions. The quality of your write-up will determine your grade (out of 15) for your reading assignment

Answers are well-written and show depth of understanding | 15 |

Answers are well-written and some, but not all, show depth of understanding | 13 |

Answers are well-written, but fail to demonstrate any depth | 11 |

Answers are not well-written or well thought-out | 9 |

### Projects

There will be one project for each topic in covered in the course. This means there will be approximately 6 projects, most of which will involve programming.Projects involve write-ups. The write-ups should be neat and thorough, yet succinct. Answering all of the questions adequately will earn you a B+. In order 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 worth 30 points. 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 |