BF778
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BF778
Physical Chemistry for Systems Biology
| course type |
Lecture |
|---|---|
| instructor | Yu (Brandon) Xia |
| time | Monday, 1:00pm - 4:00pm |
| recurrence | weekly from 2013-01-28 until 2013-04-29 |
| first session |
2013-01-28 1:00pm |
| location | PSY B51 |
Course Schedule
| date |
topics |
slides |
assignments |
solutions | deadlines |
tutorials |
|---|---|---|---|---|---|---|
| Jan 28 (Mon) |
Thermodynamics & Kinetics I |
PDF |
Tutorial 1 |
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| Feb 4 (Mon) 1:15pm-4pm |
Translational Bioinformatics (Guest Lecture by Dr. Bolan Linghu, Novartis) |
PDF |
Tutorial 2 |
|||
| Feb 11 (Mon) |
Thermodynamics & Kinetics II |
PDF |
Assignment 1 |
Solution to A1 |
Tutorial 3 |
|
| Feb 18 (Mon) |
HOLIDAY. NO CLASS. |
Tutorial 4 |
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| Feb 20 (Wed) |
Thermodynamics & Kinetics III |
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| Feb 25 (Mon) |
Thermodynamics & Kinetics IV |
PDF |
Tutorial 5 |
|||
| Mar 4 (Mon) |
Network Biology (Guest Lecture by Sara Garamszegi) |
PDF |
Assignment 2 |
Solution to A2 |
Assignment 1 due |
|
| Mar 11 (Mon) |
SPRING RECESS. NO CLASS. |
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| Mar 18 (Mon) |
Systems I |
PDF |
||||
| Mar 25 (Mon) |
Systems II |
PDF |
||||
| Apr 1 (Mon) |
Project Overview (Sara Garamszegi) |
PDF |
Complete either one: |
Assignment 2 due |
||
| Apr 8 (Mon) |
Systems III / Structure I |
PDF |
||||
| Apr 15 (Mon) |
HOLIDAY. NO CLASS. |
|
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| Apr 18 (Thur) |
CANCELLED |
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| Apr 22 (Mon) |
Structure II |
PDF |
||||
| Apr 29 (Mon) |
Structure III |
Project due |
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| May 7 (Tue) 1pm-3pm |
FINAL EXAM |
Grader
- Sara Garamszegi (sgaramsz@bu.edu)
Course Description
This course introduces students to quantitative modeling in bioinformatics and systems biology. We begin with basic principles of statistical thermodynamics, chemical kinetics, with selected applications in biomolecular systems. Next we describe molecular driving forces in biology, and computation with biomolecular structures. Finally we discuss selected quantitative models of biomolecular networks.
Required Textbook
- Molecular Driving Forces: Statistical Thermodynamics in Chemistry & Biology by Ken A. Dill and Sarina Bromberg (2002)
Recommended Books
- Physical Chemistry: Principles and Applications in Biological Sciences (4th Edition) by Ignacio Tinoco, Kenneth Sauer, James C. Wang, and Joseph Puglisi (2001)
- A Genetic Switch (3rd Edition) by Mark Ptashne
(2004)
- An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon (2006)
Recommended Online Courses
- BMI214: Representations and Algorithms for Computational Molecular Biology by Russ Altman, Stanford University
- SB228: Computational Structural Biology by Michael Levitt, Stanford University
Office Hours
After class, or by appointment.
Grading
- Homework assignments: 30%
- Programming project: 30%
- Final exam: 40%
Late Policy
All assignments and projects should be turned in to Brandon by 1PM on the due date. We will not accept late work.
