Jim Faeder (faeder@pitt.edu) BST3 3082 - Office hours: TBA
Robin Lee (robinlee@pitt.edu) BST3 3083 - Office hours: TBA
Jianhua Xing (xing1@pitt.edu) BST3 3084 - Office hours:TBA
General course questions and homework submission: csm2020-instructors@googlegroups.com.
Questions on homework: Course piazza site
Stefan Andjelkovic (stefan.andjelkovic@pitt.edu) - Office hours: W 3:30 - 4:30 pm BST3 3rd floor table
Neha Cheemalavagu (nec59@pitt.edu) - Office hours: M 10:15 - 11:15 am BST3 3rd floor table
This course will introduce students to the theory and practice of modeling biological systems from the molecular to the population level with an emphasis on intracellular processes. Topics covered include kinetic and equilibrium descriptions of biological processes, systematic approaches to model building and parameter estimation, analysis of biochemical circuits modeled as differential equations, modeling the effects of noise using stochastic methods. A range of biological models and applications will be considered including gene regulatory networks cell signaling, molecular motors, and developmental biology. Weekly recitations will introduce computational skills and provide students hands-on experience with methods and models presented in class. Course requirements include weekly homework assignments, a final project, and a take-home exam.
The course is designed for graduate and upper-level undergraduate students with a wide variety of backgrounds. The course is intended to be self-contained but students may need to do some additional work to gain fluency in core concepts. Students should have a basic knowledge of calculus, differential equations, and chemistry as well as some previous exposure to molecular biology and biochemistry. Experience with programming and numerical computation is useful but not mandatory. Laboratory exercises will use Matlab as the primary modeling and computational tool augmented by additional software as needed.
First day of class: Tuesday, January 14, 2020
Lectures: Tu,Th 9-10:30 am, BST3 3073*
Recitation/Lab: Fr 3:30-5 pm, BST3 3073*
* BST3 = Biomedical Science Tower 3 (click to see on Google maps). Building is access-controlled. If you have a Pitt ID with and RFID chip, you can ask to have building access added. If you are not a Pitt student, you will have to arrange to meet someone with access to escort you or have the guard call the main department number.
Physical Biology of the Cell, 2nd edition (PBOC2). Not required, but reading and homework assignments will be drawn from this book. We suggest you order it from your favorite online purveyor.