Fall, 2016

Course Directors

Jim Faeder (University of Pittsburgh) - faeder@pitt.edu - Office hours : after class or by appointment

Robin Lee (University of Pittsburgh) - robinlee@pitt.edu - Office hours: after class or by appointment

Andreas Pfenning (Carnegie Mellon University) - apfenning@cmu.edu - Office hours: after class or by appointment

For quickest response, please send email to csm2016-instructors@googlegroups.com.

Teaching Assistants

She Zhang - shz66@pitt.edu - Office hours: cubicles on 3rd floor of BST3 (Biomedical Science Tower)

Course Description

CMU 02-730 & PITT CMPBIO/MSCBIO 2040

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, neuroscience, population dynamics, and evolution. 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.

Prerequisites

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.

Course Requirements

  • Homework (30%)
    • Weekly graded assignments based on class lectures and readings.
    • Lateness policy: 25% credit deducted per day for late assignments. Each student will receive 3 days of grace period credit to be distributed over assignments throughout the semester. Further extensions will be granted only under extreme circumstances. All assignments must be completed to pass the course.
    • Cheating policy: All work must be your own. Unauthorized collaboration or plagiarism will result in a failing grade and will be reported to your academic advisor and dean.
  • Project (40%)
    • Model and analyze a biological network; or
    • Design and implement a simulation or analysis tool for biological modeling.
    • A project proposal will be due mid-semester. See Proposals for more information.
    • The project will be graded by peer-review panels in the final week of the course and participation in this review process will count for 25% of the project grade.
    • Cheating policy: All work must be your own and novel. Unauthorized collaboration, falsified data, or plagiarism will result in a failing grade and will be reported to your academic advisor and dean.
    • Double dipping policy: You may not re-use data, reports, manuscripts, or publications from your research or from other courses. However, you may extend your previous work, as long as you inform the instructors that you are doing so. Please contact the instructors if you have any questions regarding this policy.
  • Take-Home Exam (30%)
    • One week for a problem set covering course topics.

Meeting Times

First day of class: Tuesday, August 30, 2016.

Lectures: Tu,Th 1:30-2:50 pm, SCG 103*

Lab: Fr 1:30-3:30pm, SCG 110*

*Note: These rooms are in the Pittsburgh Supercomputing Center, 300 S. Craig Street. (directions)

Required Text

Physical Biology of the Cell, 2nd edition (PBOC). Reading and homework assignments will be drawn from this book. It has not been pre-ordered at campus bookstores, so we suggest you order it from your favorite online purveyor.

Recommended Texts

The following books may be useful as supplements to the main text and lectures.

  • Uri Alon, An Introduction to Systems Biology: Design Principles of Biological Networks, Chapman and Hall/CRC, ISBN-13: 978-1584886426.
  • Chris Myers, Engineering Genetic Circuits, Chapman and Hall/CRC, ISBN-13: 978-1420083248.
  • E. Klipp, R. Herwig, A. Kowald, C. Wierling, and H. Lehrach, Systems Biology in Practice: Concepts, Implementation, and Application, Wiley-VCH, ISBN-13: 978-3527310784. (Note: an updated version called Systems Biology: A Textbook is also now available.)
  • D. Kaplan and L. Glass, Understanding Nonlinear Dynamics. Springer. 1995. ISBN-13: 978-0387944401.
  • Eberhard Voit, A First Course in Systems Biology, Garland Science. 2012. ISBN-13: 9780815344674
  • Sarah Otto and Troy Day, A Biologist's Guide to Mathematical Modeling in Ecology and Evolution, Princeton University Press, ISBN-13: 978-0691123448
  • Athel Cornish-Bowden, Fundamentals of Enzyme Kinetics, 4th Edition (publisher's web site).

Course Outline (draft)