Computational Cell Biology

Spring 2016

CS5424 / BIOL 5424 / GBCB 5424

Objective: To learn how to build, analyze, and interpret differential equation models of molecular control systems of importance in cell biology

Instructor: Dr. Yang Cao, ycao@cs.vt.edu, 2160L Torgesen Hall,

Office Hours: MW, 9:00-10:00am.

Time and Place: 9:30 – 10:45am, Tuesday-Thursday, 230 McBryde Hall

Software: Download xpp from http://www.math.pitt.edu/~bard/xpp/xppwin.html

Reference book:

Computational Cell Biology, Christopher Fall et al., Springer, 2005

Essential Cell Biology: An Introduction to the Molecular Biology of the Cell, BRUCE ALBERTS et al., Garland Publishing Inc., 1997

and a list of journal papers

Lecture slides are only available through scholar system.

Topics to be covered

· Basic knowledge of the process of modeling and simulation

· Related topics in Mathematics (Very basic)

o ODEs

o Probability Theory

· Software: XPP, Matlab and SBML

· Typical Model

o Basic Enzyme Kinetics model

o Gene Expression Model

o basic positive and negative feedback gene circuits

o toggle switch model

o gene oscillator model

o Cell Cycle Model

o noise in a single cell

o other related biological model that you are interested

What you are required to do in this class:

· Participation (listen, think and ask) Sign-up sheet will be distributed in every class after the first week. You have a quota of three times to miss the class. After that, every time you miss a class will subject a penalty in your final grade.

· Group (two person) presentation and project

o Presentation about a published work (somebody else's work)

o A small project (that you feel interested) and the corresponding presentation

· Final: Submit two review papers (in a format of a journal paper and can be combined into one paper with both parts included)

o One is for the paper you read (a general review)

o One is for the project you did (a detailed review)

Grading policy:

My philosophy of graduate-level teaching is to offer help for students to study advanced topics. Score is recognition of your hard work. Since we will cover a broad area across: biology, physics, chemistry, mathematics, statistics, control theory and computational science, I do not expect everybody to understand everything in this class (if you do, that's great!). Thus there is no final exam. The grade will be based on class participation (50%), presentation (30%) and the small project (20%). Basically if you finish all the required work, you will get a decent score.

Honor System:

The University Honor System applies to all academic work at the university, including this course and all the assignments. For details, check http://www.honorsystem.vt.edu/.