Start Date for Spring Term: March 31st
End Date for Spring Term: June 6th.
This page describes the systems and synthetic biology elective course, 499.
http://pbd.lbl.gov/sbconf/about.php
Course Description and Objectives Syllabus
This course offers an introduction to system and synthetic biology. This course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. Students will be introduced to the field of synthetic biology and its application in systems biology and applied engineering. Students will understand in quantitative terms the basic principles of operation of regulation at the cellular level, including metabolic, signaling and gene networks; discover how cellular networks can be reengineered, taking examples from the iGEM competitions and applications such as metabolic engineering; learn how to build computer models of cellular networks; appreciate that cellular systems are very noisy, particularly bacterial systems and how these can be modeled and studied experimentally. By the end of the course students will, by simple visual inspection of a network structure, will be able to make statements on the network’s possible dynamic behavior. This ability is a prerequisite for engineering new networks.
Learn about biological parts and their properties. Understand gene and enzyme action.
Learn about network structure and pathway engineering.
Understand how synthetic networks can be simulated, built and tested in a real organism.
Learn about manipulating DNA and measuring responses.
Learn how to construct computational models and use them to study network behavior. Understand the behavior of basic network motifs found in cellular and synthetic systems, including switches, oscillators, filters, logic and pulse devices.
Learn how to build complex modular networks in silico as part of a team project.
Basic course structure:
Introduction of essential biological concepts
Kinetics of Enzyme, Protein and Gene Regulation
Network Structure, Molecular and Flux Conservation Laws
Computational Methods (simulation)
Basic Network Circuits
Experimental Techniques in Molecular Biology
Advanced Network Circuits - Bistability, Oscillators, Amplifiers, Filters and pulse generators.
Team Project to design a complex network
Jarnac Notes
Power Point Slides:
Week 1:
PowerPoint 1
PowerPoint 2
PowerPoint 3
Week 2:
Assignment 1
PowerPoint 1
Week 3:
Numerical Analysis Notes:
Solving Differential Equations
Assignment 2A
Solving Nonlinear Equations
Assignment 2B
Brief Notes on Fitting Data to Functions
Test Data for Class Exercise
Test Data
Jarnac Notes
Week 4:
Intro to Stochastic Dynamics
The Gillespie Algorithm
Assignment, Implement Gillespie Method
The Basis of the Gillespie Method
Effects of Noise
Assignment, Stochastic Simulations
Week 5:
Introduction to Synthetic Biology
BioBricks Lab, Part 1
BioBricks Lab, Part 2
Week 6:
Basic Input Devices, Lac, Lux and Tet
Bistable Circuits
Oscillator Circuits
Assignment 4 - Tet Model
Sniffers Buzzers etc Paper + MODELS
Week 7:
Logic and Feed-forward Networks
Feed-forward Networks, sequence control and Amplifiers
Motif Review by Voigt
Week 8:
Week 9:
Term Project
Final Project Report Instructions
The following documents are from last years course. See Syllabus for a description of the new syllabus.
Synthetic Biology Course Description 2007
Basic Syllabus
BioE 499 description
Link to 2007 web site:
499 Wiki, 2007
