Course: BIOEN 424: Advanced Synthetic Biology

Credits: 3

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.

 Topics Covered:

  1. The importance of network structure in cellular networks
  2. Review of continuous and stochastic models of cellular networks
  3. The interplay between structure and dynamics
  4. Bifurcation analysis and evolutionary design approaches in synthetic biology.
  5. Standards and ontologies (SBML, CellML, PoBoL, CAD in synthetic biology)
  6. Control systems in metabolism
  7. Control systems in protein networks
  8. Robustness and small signal analysis of cellular pathways
  9. Advanced structural analysis including elementary modes, FBA and MFA
  10.  Metabolic engineering strategies
  11. Protein networks, control and dynamical analysis
  12. Protein network engineering

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