MCB290 - Physical Biology of Living Organisms

Biological results are increasingly couched in the language of quantitative data. In this course we will focus on responding to such data with quantitative models. Through several classic examples we will use simple physical principles to derive quantitative models which make polarizing predictions. These predictions will then be tested by analyzing data using tools such as image analysis and bioinformatics. No previous experience with quantitative modeling or programming is necessary.

Class materials:

Download and install Matlab by logging on to the UC Berkeley Software Central

Syllabus:

Week Class date Where and when Topic Assignment Materials
1  8/26 2pm @ 301 Barker

Introduction to biological numeracy

E. coli by the numbers

Read "The Path To Biological Numeracy" section of Cell Biology by the Numbers (p. 10-30)

 

Each student present their favorite vignette from Cell Biology by the Numbers (5 minutes). Send Hernan your vignette choice by 5pm on 8/28.

Powerpoint presentation
2  9/2 2pm @ 301 Barker

Flies by the Numbers I - Part 1: Morphogen Gradients

Vignette presentations: Ignacio, Rebecca and Elizabeth

Papers: Driever1989,Liu2013

Bicoid mutant data

Matlab code

3 9/9 1pm @ 301 Barker - Note earlier start

Flies by the Numbers I - Part 2: Morphogen Gradients

 

Vignette presentations: Yang

Matlab code

4 9/14 4pm @ 547 LSA

Bacterial growth through simulations

Vignette presentations: Akshay, Rosalie, and Andy B

 

Neidhardt1999

Matlab code: Simulating bacterial growth

5 9/21 4pm @ 547 LSA

Bacterial growth through image analysis - Part 1

Vignette presentations: Andy N., Geert and Pradeep

 

Bacterial colony growth images

Matlab code: Analyzing bacterial movies

6 9/30 2pm @ 301 Barker

Bacterial growth through image analysis - Part 2

 

Vignette presentations: Diya, Chris and Jared

 
7 10/7 2pm @ 301 Barker

Flies by the Numbers II - Part 1: Lighting Up the Central Dogma

Vignette presentations: Ross, Dong and Julian

Transcriptional elongation in flies data 

8 10/14 2pm @ 301 Barker Flies by the Numbers II - Part 2: Lighting Up the Central Dogma Vignette presentations: Vanessa, Simon and Ethan Matlab code: Counting spots of nascent transcript formation
9 10/21 2pm @ 301 Barker A statistical-mechanical view of binding in biology - Part 1: Ligand-receptor and ion channels    

A First Exposure to Statistical Mechanics for Life Scientists: Applications to Binding (Garcia2007b).

Ion channel papers: Keller1986Zhong1998Perozo2002.

Ion channel data: Keller1986Data.

Ligand-receptor binding data.

Channel open probability: Matlab code.

DigitizeIt: Software to extract data from plots.

10 10/28 2pm @ 301 Barker A statistical-mechanical view of binding in biology - Part 2: Ligand-receptor and ion channels    
11 11/4 2pm @ 301 Barker A statistical-mechanical view of binding in biology - Part 3: Ligand-receptor and ion channels  

Ligand-receptor binding: Matlab code

12 11/11 No class      
13 11/18 2pm @ 301 Barker A statistical-mechanical view of binding in biology - Part 4: Hemoglobin and cooperativity  

Dimoglobin simulation: Matlab code

14 11/25 No class      
15 12/2 2pm @ 301 Barker

Regulatory biology: Transcriptional regulation in bacteria

Fill out course evaluation at https://course-evaluations.berkeley.edu!

 

Simple repression in bacteria: Oehler1994Garcia2011c.

Statistical mechanics and regulatory decision-making: Phillips2015.

Analyzing bacterial gene expression: Sample imagesSimple analysis data set.

If you're feeling adventurous about data analysis: Full data set.

 

 

 

Bibliography:

  • Phillips, R., et al. (2013). Physical Biology of the Cell, 2nd Edition. New York, Garland Science.
  • Alberts, B. (2015). Molecular Biology of the Cell. New York, NY, Garland Science.
  • Milo, R. and Phillips, R. (to be published in 2016, can be downloaded from http://book.bionumbers.org/). Cell Biology by the Numbers. New York, NY, Garland Science.
  • Mahajan, S. (2010). Street-Fighting Mathematics: The Art of Educated Guessing and Opportunistic Problem Solving. MIT Press (2010).
  • Weinstein, L. and Adam, J.A. (2008). Guesstimation: Solving the World's Problems on the Back of a Cocktail Napkin. Princeton University Press.

 

Semester: 
Fall 2015
Thursday, August 20, 2015