Modeling and Analysis of Biological Networks
With the sequencing of the human genome and the genomes of other organisms,
we now have a list of the parts that make up these biological systems.
Through the use of microarrays and other new technologies, we are also
beginning to obtain data on how genes interact with each other to perform
complex biological functions. To reason about these genetic circuits, a
systems biology perspective is necessary in which new models and efficient
analysis techniques must be developed. Given our vast experience in reasoning
about complex electronic circuits, engineers are uniquely equipped to assist
with this effort. It is not difficult to develop a view of a genetic circuit
as a electronic circuit. Such a view was taken by McAdams and Shapiro in
their seminal paper with encouraging results (Science1995).
Therefore, as in the sequencing of the human genome, collaborations between
engineers and biologists will be essential to the success of systems biology.
The goal of this course is to facilitate these collaborations by
teaching both the biological and engineering principles
necessary for such research.
Instructor: Dr. Chris Myers
Students should either have some familiarity with genetics,
cell biology, molecular biology, or biochemistry OR
engineering methods for modeling, analysis, and design. Students are not
expected to have a knowledge in both.
One is being prepared by the instructor.
- Course participation - 10 percent
- Attend class and participate in class discussions.
- Homework - 40 percent
- Will learn how to use modeling and analysis tools.
- Use simple system for tutorial.
- Choose network to champion.
- Model/analyze your network with the tool.
- Project - 50 percent
- Model and analyze a biological network, or
- Design and implement an analysis tool.
||3:40pm - 5:00pm
||1pm - 2pm
||2:30pm - 3:30pm
- Week 1: An Engineers Guide to Biology and Biochemistry
- Week 2: Phage Lambda: A Simple Genetic Circuit
- Weeks 3, 4, and 5: Learning Genetic Circuits
- Weeks 6 and 7: Stochastic Analysis
- Weeks 8 and 9: Differential Equation Analysis
- Weeks 10, 11, 12, and 13: Circuit Abstractions
- Week 14: Genetic Circuit Design
- Week 15: Project Presentations
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