7.32/7.81J/8.591J
Systems Biology

'modeling biological networks'
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Fall 2009

Lectures
(Alexander van Oudenaarden)

TR 1 - 2:30 PM
Rm. 4-163

Recitations
(Jialing Li & Bernardo Pando)

W 4 - 5 PM
Rm. 26-204

Office Hours: M 4 - 6 PM / W 5 - 6 PM
Rm. 68-377

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Problem Set #5 has been posted

(due 12/01/09 in class or
before 3 PM in Rm. 68-371)

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Course material:

Part I: Systems Microbiology
'The cell as a well-stirred bioreactor'
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• L1 - R 09/10/09 Introduction and overview
  L1_slides.pdf
  

• L2 - T 09/15/09 Michaelis-Menten kinetics, equilibrium binding, cooperativity
  L2_notes.pdf - mm.m - mmfunc.mm
  

• R1 - W 09/16/09 Basic Biology Crash Course
  R1_slides.pdf
  

• L3 - R 09/17/09 Equilibrium binding, cooperativity
  L3_notes.pdf - L3_slides.pdf
  

• L4 - T 09/22/09 Genetic engineering, ultrasensitivity by titration
  L4_slides.pdf - PubMed link
  

• Problem Set #1 (due 10/06/09)
  PS1.pdf
  

• R2 - W 09/23/09 Basic MATLAB/Math Crash Course
  R2_slides.pdf
  

• L5 - R 09/24/09 Ultrasensitivity by titration cont.
  L5_notes.pdf - L5_slides.pdf - PubMed link
  

• L6 - T 09/29/09 Positive feedback and multistability
  L6_notes.pdf - L6_slides.pdf - hasty.m - hastyfunc.m - PubMed link
  

• R3 - W 09/30/09 Problem Set #1 support

• L7 - R 10/01/09 Positive feedback and multistability cont.
  L7_notes.pdf - L7_slides.pdf - PubMed link
  

• L8 - T 10/06/09 Stability analysis and synthetic switches
  L8_notes.pdf - L8_slides.pdf - PubMed link
  

• Problem Set #2 (due 10/20/09)
  PS2.pdf
  

• R4 - W 10/07/09 Stability analysis and eigenvalues

• L9 - R 10/08/09 Synthetic genetic oscillators
  L9_notes.pdf - L9_slides - PubMed link - limitcycle.m - cyclefunc.m
  

• T 10/13/09 - No class (Monday schedule)
  

• R5 - W 10/14/09 Problem Set #2 support

• L10 - R 10/15/09 Synthetic genetic oscillators cont.
  L10_notes.pdf - L10_slides - PubMed link - routh.m
  

• L11 - T 10/20/09 E. coli chemotaxis
  L11_notes.pdf - L11_slides.pdf - PubMed link - spiro.m - spirofunc.m
  

• Problem Set #3 (due 11/03/09)
  PS3.pdf
  

• R6 - W 10/21/09 More on Oscillatory Systems
  

• L12 - R 10/22/09 E. coli chemotaxis cont.
  PubMed link
  

• L13 - T 10/27/09 Stochastic chemical kinetics
  L13_notes.pdf
  

• R7 - W 10/28/09 Problem Set #3 support

• L14 - R 10/29/09 Stochastic chemical kinetics cont.
  same notes as L13 (L13_notes.pdf)
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Part II: Cell Systems Biology
'The importance of diffusion and gradients for cellular regulation'

• L15 - T 11/03/09 Introduction Cell Systems Biology, Diffusion, Fick's Law
  L15_notes.pdf - L15_slides.pdf

• Problem Set #4 (due 11/17/09)
  PS4.pdf
  

• R8 - W 11/04/09 Stochastic simulations using MATLAB
  R8.pdf - first_matlab_simulation.m
  

• L16 - R 11/05/09 Local excitation, global inhibition theory
  L16_notes.pdf - turing.m
  

• L17 - T 11/10/09 Local excitation, global inhibition theory cont.
  L17_slides.pdf
  

• R9 - W 11/11/09 no recitation (Veteran's day)

• L18 - R 11/12/09 Rapid pole-to-pole oscillations in E. coli
  L18_slides.pdf - how_eig.m - how_homog.m
  

• L19 - T 11/17/09 Rapid pole-to-pole oscillations in E. coli cont.
  L19_slides.pdf
  

• Problem Set #5 (due 12/01/09)
  PS5.pdf
  

• R10 - W 11/18/09 Traveling waves in reaction-diffusion systems

• L20 - R 11/19/09 Models for eukaryotic gradient sensing
  L20_slides.pdf
  

• L21 - T 11/24/09 Modeling cytoskeleton dynamics
  L21_slides.pdf - PubMed link
  

• R11 - W 11/25/09 Problem Set #5 support

• R 11/26/09 no class (Thanksgiving day)

• L22 - T 12/01/09 Modeling cytoskeleton dynamics cont.
  

• Final Problem Set (due 12/10/09)
  

• R12 - W 12/02/09 Modeling microtubule dynamics

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Part III: Developmental Systems Biology
'Building an organism starting from a single cell'

• L23 - R 12/03/09 Embryonic development
  

• L24 - T 12/08/09 Embryonic development cont.
  

• R13 - W 12/09/09 Final problem set support
  

• L25 - R 12/10/09 Embryonic development cont.

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