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: TBD Teaching AssistantsKelvin Liu  Marcus Thomas  Course DescriptionCMU 02730 & 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, modeling spatial effects, and modeling
at higher levels of abstraction or scale using logical or agentbased
approaches. A range of biological models and applications will be
considered including gene regulatory networks, cell signaling, cell
cycle regulation, and pharmacokinetics
and pharmacodynamics (PK/PD). Weekly lab sessions will provide students
handson experience with methods and models presented in class. Course
requirements include regular class participation, weekly homework
assignments, a takehome exam, and a final project. PrerequisitesThe
course is designed for graduate and upperlevel undergraduate students
with a wide variety of backgrounds. The course is intended to be
selfcontained 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.
 TakeHome Exam (30%)
 One week for a problem set covering course topics.
 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 midsemester. See Proposals for more information.
 The project will be graded by peerreview 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 reuse 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.
Meeting TimesFirst day of class: Tuesday, September 1, 2015. Lectures: Tu,Th 1:302:50 pm, SCG 103*
Lab: Fr 1:303:30pm, SCG 110*
*Note: These rooms are in the Pittsburgh Supercomputing Center, 300 S. Craig Street. (directions)
Please see Course Calendar for additional details. Course Outline (tentative) Introduction
 Systems Biology (Faeder) [1 lecture]
 Introduction to Mathematical Modeling (Langmead) [1 lecture]
 Modeling Formalisms (Langmead) [2 lectures]
 Analysis of ODEs (Faeder) [2 lectures]
 Parameter Estimation (Langmead) [3 lectures]
 Biochemical Kinetics (Faeder) [3 lectures]
 Modeling Genetic Circuits (Faeder) [2 lectures]
 Modeling Stochasticity (Faeder) [2 lectures]
 Modeling Cell Signaling (Faeder) [1 lecture]
 Modeling the Cell Cycle (Faeder) [1 lecture]
 Spatial Modeling with PDEs (Langmead) [1 lecture]
 Spatial Stochastic Modeling (Faeder) [1 lecture]
 Population Models & Evolutionary Dynamics (Langmead) [2 lectures]
 Markov Models (Langmead) [2 lectures]
 PK/PD Modeling (Langmead) [1 lecture]
 Project Presentations (students) [2 lectures]
Recommended TextsThe 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, ISBN13: 9781584886426.
 Chris Myers, Engineering Genetic Circuits, Chapman and Hall/CRC, ISBN13: 9781420083248.
 E. Klipp, R. Herwig, A. Kowald, C. Wierling, and H. Lehrach, Systems Biology in Practice: Concepts, Implementation, and Application, WileyVCH, ISBN13: 9783527310784. (Note: an updated version called Systems Biology: A Textbook is also now available.)
 D. Kaplan and L. Glass, Understanding Nonlinear Dynamics. Springer. 1995. ISBN13: 9780387944401.
 Eberhard Voit, A First Course in Systems Biology, Garland Science. 2012. ISBN13: 9780815344674
 Sarah Otto and Troy Day, A Biologist's Guide to Mathematical Modeling in Ecology and Evolution, Princeton University Press, ISBN13: 9780691123448
