Fall, 2017

Course Directors 

Jim Faeder (University of Pittsburgh) - faeder@pitt.edu - BST3 3082 - Office hours: Fridays, 1-3 pm.
Robin Lee (University of Pittsburgh) - robinlee@pitt.edu - BST3 3083 - Office hours: by appointment.
Jianhua Xing (University of Pittsburgh) - xing1@pitt.edu - BST3 3084 - Office hours: by appointment.

For quickest response, please send email to csm2017-instructors@googlegroups.com

Teaching Assistants

Kunal Aggarwal -  kua5@pitt.edu - BST3 3076.22 (cubicle) - Office hours: Mondays, 12-1 pm.
Chaitanya Mokashi - chaitanya.mokashi@pitt.edu - BST3 3076.26 (cubicle) - Office hours: Mondays, 4:30-5:30 pm.

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, 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%) 
    • 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 29, 2017
Lectures: Tu,Th 10:30am - noon, BST3 3073* 
Recitation/Lab: Fr 9-10:30am, 
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.

Required Text

Physical Biology of the Cell, 2nd edition (PBOC2). 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

WeekDayDateTitlePresenterReading (#'s refer to PBOC2)
1Tuesday8/29/2017Intro to systems biologyLeepapers
Thursday8/31/2017Introduction to thermodynamics of cellsFaeder5
Friday9/1/2017RecitationTA
2Monday9/4/2017HW 1 due
Tuesday9/5/2017Boltzmann distribution and equilibrium bindingFaeder6.1-6.2
Thursday9/7/2017BionumbersXing3,4
Friday9/8/2017RecitationTA
3Monday9/11/2017HW 2 due
Tuesday9/12/2017Law of mass action, simple binding, Hill functionFaeder6.3-6.4
Thursday9/14/2017Two-state systems, cooperativity, allosteryFaeder7.1-7.3
Friday9/15/2017RecitationTA
4Monday9/18/2017HW3 due
Tuesday9/19/2017Dynamics of Transcriptional Motifs 1Lee
Thursday9/21/2017Dynamics of Transcriptional Motifs 2Lee
Friday9/22/2017RecitationTA
5Monday9/25/2017HW 4 due
Tuesday9/26/2017Dynamics of Transcriptional Motifs 3Lee
Thursday9/28/2017Biochemical Kinetics 1Faeder15.1-15.2
Friday9/29/2017RecitationTA
6Monday10/2/2017HW5 due
Tuesday10/3/2017Biochemical Kinetics 2Faeder15.3-15.4
Thursday10/5/2017Boolean modelingMiskov-Zivanov
Friday10/6/2017RecitationTA
7Monday10/9/2017No HW (Fall break)
Tuesday10/10/2017No class (Fall break)
Thursday10/12/2017Macromolecules 1Xing8
Friday10/13/2017RecitationTA
8Monday10/16/2017Project proposals due
Tuesday10/17/2017Macromolecules 2Xing8
Thursday10/19/2017DiffusionXing13
Friday10/20/2017Recitation
9Monday10/23/2017HW6 due
Tuesday10/24/2017Motor Mechanics 1Xing16
Thursday10/26/2017Motor Mechanics 2Xing16
Friday10/27/2017RecitationTA
10Monday10/30/2017HW7 due
Tuesday10/31/20172D ODE's 1Faeder19.3
Thursday11/2/20172D ODE's 2Faeder19.3, Kaplan and Glass
Friday11/3/2017RecitationTA
11Monday11/6/2017HW8 due
Tuesday11/7/2017Parameter estimation Gupta
Thursday11/9/2017Stochasticity/ CMEFaeder19.3
Friday11/10/2017RecitationTA
12Monday11/13/2017HW9 due
Tuesday11/14/2017Spatial dynamics 1Faeder20.1-20.3
Thursday11/16/2017Spatial dynamics 2Faeder
Friday11/17/2017RecitationTA
13Monday11/20/2017HW 10 due
Tuesday11/21/2017No class (Projects)
Thursday11/23/2017No class (Thanksgiving)
Friday11/24/2017No recitation (Thanksgiving)
14Tuesday11/28/2017Case study IXing
Thursday11/30/2017Case study 2Faeder
Friday12/1/2017Final Projects Reports Due
15Monday12/4/2017Preliminary project scores due
Tuesday12/5/2017No class

Thursday12/7/2017Project reviewing
Faeder/Lee
Friday12/8/2017Take home exam distributed
16Wednesday12/13/2017Take home exam due
Wednesday12/20/2017Final Grades Due

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