Cell and Systems Modeling

Spring, 2020

CMU 02-730 & PITT CMPBIO/MSCBIO 2040

Course Directors

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

Teaching Assistants

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

Course Description

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.

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%)
    • Bi-weekly graded assignments based on class lectures and readings.
    • Lateness policy: 25% credit deducted per day for late assignments. Each student will receive 5 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 (30%)
    • 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.
  • Class Participation (10%)

Meeting Times

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.

Textbook

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.

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).