From BiocircuitsWiki

BioCircuits: A Systems Approach to Synthetic Biology

Instructor: Eric Klavins Assistant Professor Electrical Engineering Office Hours: Fr: 11:30-12:30 and by appointment Office Location: EE B040 Teaching Assistants: Paul Ryan Josh Bishop Rob Egbert Brandi House Kevin Oishi Course Number: EE 400F (undergrads) EE 546A (grads)

Lecture: MWF 10:30-11:20 am Room MEB 234 Lab: A: Tu 3:30-6:30 and We 11:30-2:30 B: We 3:30-6:30 and Th 11:30-2:30 Room EE B031 (Lower Basement of EE) Note: Lab sections are not listed in UW course guide

What is synthetic biology? Click here.

Grading

Final Projects

• Du: Sensing Gene Expression Patterns with Genetic Finite State Machines
• Galuska: Using Directed Evolution to Build a Flip-Flop in E. coli
• Knight: An E. coli Multiplexer
• Olson: Use of Toxin-Antitoxin systems for a robust genetic oscillator
• Penkov: Engineering bacteria to attack tumors
• Xu: Nucleic Acid Based Data Structures
• Zhang: A Pseudo-biological Arithmetic Logic Unit

Final Lab Results Are In!

After seven weeks of learning how to do work with genes and bacteria, the lab groups spent the last week on a special project: (a) To extract an interesting gene of their choice from 'E. coli; (b) to put it into a biobrick plasmid with an IPTG inducible promoter; (c) to make a prediction about how over expression of the gene would affect growth and to test that prediction. Almost all the teams achieved (a) and (b), although some team's sequencing results were more convincing than others and a few of the genes were just plain hard to work with. At least two teams, noted below, also clearly achieved (c). Congratulations!

• Nielsen and Lee: rodZ
• America and Coult: minE -- growth prediction confirmed!
• White and Galuska: asr (part 1), asr (part 2)
• Jang and Olsen: yafQ
• Sheperd and Thompson: sdia
• Duncombe and Renneberg: zapB
• Zhang and Tobe: yhaV -- biobrickable! -- growth prediction confirmed!
• Du and Penkov: mreC
• Knight and Xu: chpB -- biobrickable!

Description

BioCircuits is an introduction to the theory and practice of building artificial biochemical reaction networks and devices. BioCircuits have applications in cell and tissue engineering, gene therapy, biologically derived drugs and materials, alternative fuels, biosensors, and much more. Presently artificial biochemical devices and circuits are difficult to design, behave unpredictably, and are difficult to analyze; however new tools and approaches are emerging rapidly and promise to make engineering living systems and components broadly useful. Many of these emerging tools are based on tools in computer science (digitial logic, automata theory) and electrical engineering (circuit theory, feedback control, signal processing, dynamical systems).

The course is open to all engineering students and does not assume any background in biology or chemistry. It will consist of a lecture and a lab. The lab will consist of about six hours a week in the lab (EE B031) and 3 hours working on lab reports and data analysis.

Lecture

The lecture component of the course is an introduction to modeling, simulation, analysis, and design of biochemical devices, regulatory networks, and signaling systems (i.e. biocircuits). Topics will include

• an overview of the molecular biology of bacteria;
• the theory of chemical kinetics and biochemical reaction networks;
• analog and digital-logic biocircuits;
• design techniques for building novel biocircuits.
• stochastic processes inside the cell and single cell techniques
• system identification and parameter estimation

Lab

There will be an intensive laboratory component to this course for students wanting to build their own synthetic organisms. Topics include:

• biochemical sensors, effectors, and other mechanisms;
• genetic engineering in bacteria;
• the design and construction of biocircuits encoded in DNA from standard parts;
• measurement of the dynamic behavior of biocircuits expressed in populations and in single cells.

Prerequisites

The course is open to all juniors, seniors, and graduate students who have a background in circuits, computer architecture, control systems, signal processing, dynamical systems, applied math, bioengineering, or mathematical biology. No background in chemistry or biology will be assumed.

Laboratory Schedule

We are planning to have two lab sections (which are not listed in the online course listing):

• Section A meets both Tu: 3:30-6:30 and We: 11:30-2:30
• Section B meets both We: 3:30-6:30 and Th: 11:30-2:30

Textbooks (Optional)

• Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman & Hall/CRC, 2006.

• Nelson and Cox, Principles of Biochemistry, 4th Edition, Freeman, 2004.

• Course notes by the instructor are here.

FAQ

• Q: I am a CSE graduate student. Does this course count for my quals requirement?
• A: In the past, CSE has approved this course as fulfilling one of the "post-quals" course requirements. Contact the CSE grad advisor or quals committee for details.

• Q: How much time is this course going to take?
• A: The lecture is a standard course with weekly homeworks, readings and (for graduate students taking 546) a light project. It is intended to be a gentle introduction to the subject, concentrating on fundamentals. The lab is more strenuous and will include about 6 hours per week in the lab and about 3 hours per week of preparation and data analysis.

• Q: How is the lecture part of the course structured?
• A: Chalk and talk lectures, weekly readings, mathy homeworks, and a course project.

• Q: What are BioCircuits and how they are being used today?
• A: Everything from HIV treatments to increasing ethanol production in corn. Your body is filled with biocircuits that make you go. See http://www.igem.org/ for some ideas of the crazy things students in classes like this are doing.

• Q: How “intensive” is the lab? What kind of projects will be done in it?
• A: The lab is at least six hours a week. You will learn basic genetic engineering and DNA manipulation. This involves culturing bacteria, cutting apart and recombining DNA, transforming bacteria, looking at your transformed cells under a microscope to get time series data of their behavior, fitting models to the resulting data, etc. It is a lot of fun and a lot of work/time.

• Q: My knowledge is limited to 200 level EE courses (271, 235, 233, and 215); is this sufficient?
• A: Your knowledge is sufficient. The real question is whether you are okay with a conceptually difficult and open-ended class. There is no plug-and-chug in this course. You will have to be creative and will likely have to wrap your head around new concepts every day. These concepts will be new to more advanced students too, but those students may have better "learned to learn" already.

The old BioCircuits page is here.