BE 150/Bi 250b Winter 2012

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WARNING: This page is for a previous year.
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Systems Biology

Instructors

  • Michael Elowitz (Bi/BE/APh)
  • Richard Murray (CDS/BE)
  • Lectures: MW 10-11, 101 Kerckhoff

Teaching Assistants

  • Emzo de los Santos
  • Vanessa Jonsson
  • Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)

Lecture Schedule

There will be two 1-hour lectures each week, as well as a 1-hour recitation section.

Week Date Topic Reading Homework
1
4 Jan
6 Jan+
MBE/RMM
Course overview
  • Principles in systems biology

Recitation section:

  • MATLAB tutorial (optional)

Matlab Tutorial

Bi 250b:

  • Alon, Ch 1: Introduction

BE 150:

  • BFS, Ch 1: Introductory Concepts
  • BFS, Ch 2: Modeling of Core Processes
    • Section 2.1: Modeling Techniques
2
9 Jan
11 Jan+

MBE
Gene circuit dynamics
  • Core processes in cells
  • Modeling transcription, translation and regulation using ODEs
  • Negative auto-regulation

Bi 250b:

  • Alon, Ch 2: Transcription networks : basic concepts
  • Alon, Ch 3: Autoregulation : a network motif

BE 150:

  • BFS, Ch 2: Modeling of Core Processes
    • Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:

BEHW1 BIOHW1
3
16 Jan
18 Jan*
20 Jan*

RMM
Circuit motifs
  • Feedforward loops (FFLs)
  • Phosphorylation cascades
  • Two-component signaling systems
  • Sequestration for ultrasensitivty

Bi 250b:

  • Alon, Ch 4: The feed-forward loop network motif
  • Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:

  • BFS, Ch 2: Modeling of Core Processes
    • Section 2.4: post-transcriptoinal regulation
    • Section 2.5: cellular subsystems

Papers discussed in lecture:

BEHW2 BIOHW2
4
23 Jan
25 Jan

MBE
Biological clocks: how to produce oscillations in cells
  • Plant clocks/circadian rhythm
  • Synthetic oscillators (repressilator, dual-feedback oscillator)
  • Circadian clocks in cyanobacteria

BE 150:

  • BFS, Ch 3: Analysis of Dynamic Behavior
    • Sections 3.5: Oscillatory Behavior
BEHW3 BIOHW3
5
30 Jan
1 Feb

RMM
Robustness
  • Chemotaxis and perfect adaptation
  • Fold change detection
  • Controls analysis of robustness

BE 150:

BE150 HW #4 Bi250b HW#4
6
6 Feb*
8 Feb

RMM
Noise
  • Random processes
  • Intrinsic and extrinsic noise
  • Stochastic modeling: master equation, SSA

BE 150:

BEHW5 BIOHW5

7
13 Feb+
15 Feb

MBE
Burstiness in gene expression and signalling
  • Birth-death processes
BEHW6 BIOHW6
8
20 Feb
22 Feb
24 Feb

RMM
Patterning
  • Morphogenesis
  • Robust morphagen gradient
  • Proportionality and scaling
BEHW7 BioHW7
9
27 Feb
29 Feb*+

MBK
Modeling of complex biological networks (Mary Kennedy)
10
5 Mar
7 Mar+
MBE
Fine grain patterns
  • Lateral inhibition
  • Notch-delta
BEHW8 BioHW8


Course Description

BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

BE 150: Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

Bi 250b: The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

Textbook

The primary text for the BE 150 and Bi 250b is

 [Alon]  U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press, 2006.

Students in BE 150 should also obtain the following notes (freely downloadable from the web):

 [BFS]  D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
  • Note: these notes are being written and will be updated during the course
  • Class version (Caltech access only, 29 Jan 2012): TOC, Ch 1, Ch 2, Ch 3, Ch 4, Sec 5.2, App C, Refs

The following additional texts and notes may be useful for some students:

 [FBS]  K. J. Astrom and R. M. Murray, Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki.
 [Klipp]  Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, Systems biology: A textbook. Wiley, 2009.
 [Strogatz]  Steven Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering. Westview Press, 2001.

Grading

The final grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

Collaboration Policy

Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reflect your understanding of the subject matter at the time of writing.