7.81/8.591/9.531
Systems Biology

'modeling biological networks'
_________________________

Fall 2007

Lectures
(Alexander van Oudenaarden)

TR 1 - 2:30 PM
Rm 2-105

Recitations
(Rui Zhen Tan & Shankar Mukherji)

W 4 - 5 PM
Rm 26-204

Office Hours: M 4 - 6 PM
Rm 68-377

_________________________

The final PS is due T 12/11/07
(before 3PM in class or Rm. 68-371)

_________________________

Course material:

Part I: Systems Microbiology
'The cell as a well-stirred bioreactor'
______________________________

• L1 - R 09/06/07 Introduction and overview
  L1_slides.pdf
  

• L2 - T 09/11/07 Michaelis-Menten kinetics, equilibrium binding, cooperativity
  L2_handout.pdf - mm.m - mmfunc.m
  

• R1 - W 09/12/07 Basic Biology Crash Course
  R1_handout.pdf
  

• L3 - R 09/13/07 Equilibrium binding, cooperativity
  L3_slides.pdf
  

• L4 - T 09/18/07 Lambda phage, multistability
  L4_slides.pdf - L4_handout.pdf - hasty.m - hastyfunc.m
  

• Problem Set #1 (due 10/02/07)
  ps1.pdf - ps1_1.m - ps1_2.m - ps1_2_fLHS.m
  

• R2 - W 09/19/07 Basic MATLAB/Math Crash Course
  R2_handout.pdf
  

• L5 - R 09/20/07 Cellular memory and hysteresis, the lac operon
  L5_slides.pdf - L5_handout.pdf
  

• L6 - T 09/25/07 Bistability in the lac operon
  same material as L5
  

• R3 - W 09/26/07 Problem Set #1 support

• L7 - R 09/27/07 Synthetic gene switches, Stability analysis
  L7_slides.pdf - L7_handout.pdf
  

• L8 - T 10/02/07 Modeling E. coli chemotaxis
  L8_slides.pdf - L8_handout.pdf - spiro.m - spirofunc.m
  

• Problem Set #2 (due 10/18/07)
  ps2.pdf
  

• R4 - W 10/03/07 Stability analysis and eigenvalues

• L9 - R 10/04/07 no lecture

• T 10/09/07 - Columbus day vacation
  

• R5 - W 10/10/07 no recitation

• L10 - R 10/11/07 Modeling E. coli chemotaxis cont.
  same notes/handout as L8
  

• L11 - T 10/16/07 Synthetic genetic oscillators
  L11_slides.pdf - L11_handout.pdf - limitcycle.m - cyclefunc.m
  

• R6 - W 10/17/07 Problem Set #2 support
  

• L12 - R 10/18/07 Synthetic genetic oscillators cont.
  L12_slides.pdf - L12_handout.pdf - routh.m
  

• Problem Set #3 (due 11/01/07)
  ps3.pdf
  

• L13 - T 10/23/07 Stochastic chemical kinetics
  L13_slides.pdf - L13_handout.pdf
  

• R7 - W 10/24/07 Stochastic chemical kinetics

• L14 - R 10/25/07 Stochastic chemical kinetics cont.
  same notes/handout as L13

______________________________

Part II: Cell Systems Biology
'The importance of diffusion and gradients for cellular regulation'

• L15 - T 10/30/07 Introduction Cell Systems Biology, Diffusion, Fick's Laws
  L15_slides.pdf - L15_handout.pdf
  

• R8 - W 10/31/07 Problem Set #3 support
  

• L16 - R 11/01/07 Local excitation, global inhibition theory
  L16_handout.pdf
  

• Problem Set #4 (due 11/13/07)
  ps4.pdf
  

• L17 - T 11/06/07 Local excitation, global inhibition theory cont.
  L17_slides.pdf - turing.m
  

• R9 - W 11/07/07 Reaction-diffusion equations

• L18 - R 11/08/07 Rapid pole-to-pole oscillations in E. coli
  L18_slides.pdf - how_homog.m - how_eig.m
  

• L19 - T 11/13/07 Rapid pole-to-pole oscillations in E. coli cont.
  L19_slides.pdf
  

• Problem Set #5 (due 11/27/07)
  ps5.pdf - ps5_1.m - ps5_2.m - laplacian2dperiodic.m
  

• R10 - W 11/14/07 Numerical simulations

• L20 - R 11/15/07 Models for eukaryotic gradient sensing
  L20_handout.pdf - L20_slides.pdf - narang.m
  

• L21 - T 11/20/07 Models for eukaryotic gradient sensing cont.
  L21_slides.pdf
  

• R11 - W 11/21/07 Problem Set #5 support

• L22 - T 11/27/07 Modeling cytoskeleton dynamics
  L22_slides.pdf
  

• Final Problem Set (due 12/11/07)
  final_ps.pdf
  

• R12 - W 11/28/07 Modeling microtubule dynamics

• L23 - R 11/29/07 Modeling cytoskeleton dynamics cont.
  same notes as L22
  

• L24 - T 12/04/07 Modeling cytoskeleton dynamics cont.
  L24_slides.pdf
  

• R13 - W 12/06/07 Final problem set support
  

______________________________

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

• L25 - R 12/06/07 Drosophila development
  L25_slides.pdf
  

• L26 - T 12/11/07 Drosophila development cont.
  L26_slides.pdf
  

______________________________