Course: BIOEN 424: Advanced Synthetic Biology
Instructor: Herbert Sauro
Texts and Supplemental Materials: No official text book but the following can be recommended:
* U. Alon, Control Systems Engineering, An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman and Hall, 2006.
* Systems Biology: A Textbook. (ISBN-10: 3527318747) Klipp et al
* Engineering Genetic Circuits (ISBN-10: 1420083244) Myers.
* Enzyme Kinetics for Systems Biology. Sauro HM ($39 but available for approximately $6 to students in this course)
This course also involves extensive reading and discussion of papers from the synthetic biology world.
UW Catalog Description: Covers advanced concepts in system and synthetic biology. Includes kinetics, modeling, stoichiometry, control theory, metabolic systems, signaling, and motifs. All topics are set against problems in synthetic biology. Offered: jointly with EE 424/CSE 487
Prerequisites by Course: Either BIOEN 401, BIOEN 423, EE 423, or CSE 486.
Prerequisites by Topic: Introductory Synthetic Biology
Required or Elective: Elective
Specific Outcomes: At the end of this course, students will be able to:
- Understand the different modeling approaches used to represent cellular networks (Structural, Continuous and Stochastic Approaches)
- Understand the differences between the fundamental cellular subsystems, metabolic, protein and genetic and how this influences potential engineering approaches.
- Develop an appreciation for the need for standards and ontologies in model exchange and part representation.
- Understand, implement and use a variety of computational approaching including FBA, MFA, Bifurcation and evolutionary methods.
- Understand the basic principles of metabolic control including small signal analysis and elementary mode analysis.
- Learn how to carry out a robustness analysis of a metabolic pathway and propose strategies for engineering pathways.
- Understand the control of protein networks, highlighting differences and similarities with genetic and metabolic systems.
- Use computational analysis to study the dynamic properties of protein networks and the design of robust systems.
Outcomes Addressed by this Course:
A. An ability to apply knowledge of mathematics, science, and engineering.
C. An ability to communicate effectively.
L. An understanding of biology and physiology.
- The importance of network structure in cellular networks
- Review of continuous and stochastic models of cellular networks
- The interplay between structure and dynamics
- Bifurcation analysis and evolutionary design approaches in synthetic biology.
- Standards and ontologies (SBML, CellML, PoBoL, CAD in synthetic biology)
- Control systems in metabolism
- Control systems in protein networks
- Robustness and small signal analysis of cellular pathways
- Advanced structural analysis including elementary modes, FBA and MFA
- Metabolic engineering strategies
- Protein networks, control and dynamical analysis
- Protein network engineering