BE 150/Bi 250 Spring 2014

Systems Biology
Instructors Michael Elowitz (Bi/BE/APh) Richard Murray (CDS/BE) Lectures: MWF 11-12, 200 BRD	Teaching Assistants Victoria Hsiao (BE) Vipul Singhal (CNS) Recitation: Fr 11-12, location TBD
This is the course homepage for BE 150/Bi 250 for Spring 2014. This page contains all of the information about the material that will be covered in the class, as well as links to the homeworks and information about the course projects and grading.

WARNING: This page is still under construction. This banner will be removed when things are finalized.

Lecture Schedule

There will be 2-3 one-hour lectures each week, as well as occasional one-hour tutorials, recitations or journal club.

Week	Date	Topic	Reading	Homework
1	31 Mar 2 Apr MBE/RMM	Course overview, gene circuit dynamics Introduction to the course Rate equations enable analysis of gene regulation circuits Degradation rates control response times in simple open-loop gene regulation Autoregulatory feedback loops modulate the response times of genetic circuits, limit variability, and can enable rate-responsive systems Cooperative responses can enable switch-like regulation and bistability Circuit motifs can help identify functional modules in complex circuits Recitation section: 5 Apr MATLAB and SimBiology Tutorial Useful MATLAB commands: useful_matlab.m SimBiology example: rec1_pos_regdemo.sbproj MATLAB/ode45 example: pos_reg_main.m, pos_reg.m Simbiology Tutorial	Bi 250b: Alon, Ch 1: Introduction Alon, Ch 2: Transcription networks : basic concepts Alon, Ch 3: Autoregulation : a network motif BE 150: BFS Ch 1: Introductory Concepts (skim) BFS Ch 2: Modeling of Core Processes Section 2.1: Modeling Techniques (skim) Sections 2.2-2.3: transcription and translation, transcriptional regulation
2	7 Apr 11 Apr* RMM	Circuit motifs Feed-forward loops enable temporal filtering and pulse generation ‘Futile cycles’ generate zero-order ultrasensitivity (phospho-switches) Multi-gene positive feedback loops can enable toggle switch behaviors Positive feedback can generate hysteresis and irreversibility - example: Xenopus oocyte maturation Paradoxical regulation by cytokines could enable regulation of a population response Recitation (9 Apr): sample problems MATLAB/curve fitting tool example: cftools_example.m	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-transcriptional regulation Section 2.5: cellular subsystems
3	14 Apr+ 16 Apr+ MBE	Robustness Critical features of genetic circuits may be robust to variation in their own components, and the principle of robustness can be used to select identify likely circuit architectures: In the bacterial chemotaxis circuit, perfect adaptation is robust to fluctuations in key cellular components Bifunctional kinases can generate ideal linear amplifiers with robustness to component concentrations Cosubstrate competition provides oxygen homeostasis across a broad range of oxygen levels (Kueh) Recitation (1 Feb): sensitivity analysis Demo of sensitivity analysis and how to add events in simbio: I1FFL_sens_event_demo.sbproj Demo of how to use compartments within one model: multiple_compartments.sbproj	Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis BE 150: BFS Ch 3: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations) BFS Sec 5.2: Bacterial chemotaxis
4	21 Apr 23 Apr+ MBE	Guest lecture: Joe Markson Clock-like oscillations can be implemented in cells: Delayed negative feedback can enable clock-like oscillations in individual cells (Repressilator) Combined positive/negative feedback enables relaxation oscillation whose period and amplitude can be tuned independently A simple three-protein system can generate accurate clock-like oscillations of phosphorylation state April 25: Course Project Assignments	BE 150: BFS Ch 3: Analysis of Dynamic Behavior Sections 3.5: Oscillatory Behavior
5	28 Apr 30 Apr RMM	Stochasticity, or ‘noise’ is ubiquitous in genetic circuits: Intrinsic noise (stochasticity) in gene expression limits the accuracy of gene regulation Variability can be controlled by altering burst parameters	BE 150: BFS Ch 4: Stochastic behavior App B: Probability and random processes (optional)
6	5 May* 7 May* RMM	Stochastic pulsing provides multiple functions in cells, similar to the role of oscillatory signals in engineering Frequency modulation coordinates the responses of diverse genetic targets (example: yeast stress response) Excitability is a noise-dependent mechanism that enables probabilistic control of transient, stereotyped differentiation events Pulsing can enable dynamic multiplexing (example: p53)
	9 May	Course project discussion with TAs
7	12 May 14 May MBE	Guest Lecture: Sandy Nandagopal & Joe Markson Patterning Cis inhibition can enforce heterotypic signaling (example: The Notch signaling pathway) Morphogen Shuttling can enable robust scaling (example BMP signaling)	Alon, Ch 8: Robust Patterning in Development
8	19 May 21 May MBE	Project presentations
9	28 May+ 30 May*	Project presentations

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) Note: these notes are being written and will be updated during the course The public version is missing some copyrighted figures. These are available in the class version. Class version (Caltech access only, 5 Jan 2013): TOC, Ch 1, Ch 2, Ch 3, Ch 4, Sec 5.2, App B, Refs

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

[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.

Course project

All students enrolled in the course will be expected to participate in a course project, which will be assigned after the fourth week of class. Course projects will generally consist of reviewing one or more papers on a topic that makes use principles and tools discussed in the course. Each project will be undertaking by two students (nominally one from BE 150, one from Bi 250). Topic suggestions are posted here. Students can also propose their own topic of student by preparing a 1-2 page proposal and submitting this to the instructors no later than 4 Feb for consideration.

Course project timeline:

• 1 Feb (Fri): course projects posted on home page and announced in class
• 4 Feb (Mon): course project preferences due
• 6 Feb (Wed): project assignments available
• 20 Feb (Wed): discussion of course projects with TAs and others
• 4-13 Mar: course project presentations. 15-20 minutes per project + 5-10 minutes questions.

Course preference instructions

• Each student should send e-mail no later than 4 Feb (Mon) with the following information
  • Course: (BE 150/Bi 250b/Audit)
  • Up to three project preferences (use titles from project listings)
  • Optional preferred partner (both students should e-mail identical preferences)
• Students will work in pairs, with most teams consisting of a BE 150 student and a Bi 250b student
• To propose your own project, please e-mail a 1-2 page proposal in addition to at least two project preferences selected from the list of course projects

Grading

The final grade will be based on biweekly homework sets (75%) and a course project (25%). The homework will be due in class approximately 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. The class project will be assigned and the end of the 5th week of instruction and project presentations will be scheduled for the last two weeks of class.

Collaboration Policy

Collaboration on homework assignments and the course project 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. Your course project presentation to properly acknowledge all source materials.