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BioCircuits will be offered in the Spring of 2008 for the 2nd time. It is open to all engineering students and does not assume any background in biology or chemistry. It will consist of a mandatory lecture (EE 400 B, open to 50 students) and an optional lab (EE 400 C open to 20 students). 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. We will report our lab results back to the lecture so that students not doing the labs can see what's going on.
Description
BioCircuits is an introduction to the theory and practice of artificial biochemical reaction networks and devices, also known as synthetic biology. BioCircuits have applications in cell and tissue engineering, gene therapy, biologically derived drugs and materials, alternative fuels, biosensors, and much more. Presently BioCircuits are difficult to design, behave unpredictably, and are difficult to analyze; however new tools and approaches are emerging that promise to make engineering BioCircuits broadly useful. These emerging tools are based on tools in computer science (digitial logic, automata theory), electrical engineering (circuit theory, feedback control, signal processing, dynamical systems).
Lecture
The lecture component of the course is an introduction to modeling, simulation, analysis, and design of biochemical devices and circuits. Topics will include
- an overview of the molecular biology of bacteria;
- the theory of biochemical reaction networks;
- analog and digital-logic biocircuits;
- design techniques for building novel biocircuits.
Lab
There will be an intensive (but optional) 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 from standard parts;
- measurement of the dynamic behavior of biocircuits expressed in single cells.
Prerequesites
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 or mathematical biology. No background in chemistry or biology will be assumed.
Laboratory Schedule
Textbooks
- 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.
FAQ
- Q: I am a CSE graduate student. Does this course count for my quals requirement?
- A: Yes. CSE has approved this course. Contact the CSE quals committee for details.
- Q: How much time is this course going to take?
- A: The lecture is a standard 4 credit course with weekly homeworks, readings and a light project. It is intended to be a gentle introduction to the subject, concentrating on fundamentals. The optional 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: Weekly readings, homeworks, and a course project. No exams.
- Q: What BioCircuits are or 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 these 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.
