Course: BIOEN 498: Fundamentals of Synthetic Biology

(Provisional/Tentative – please note this course is in the process of evolving)

Credits: 3

Instructor: Herbert Sauro

Texts and Supplemental Materials: No textbook.  Online video tutorials will be available to enrolled students

UW Catalog Description: Topics of current interest in the field, offered as lectures, conferences, or laboratory.

Prerequisites by Topic:  Basic math and biology. Knowledge of at least one programming language, eg MATLAB

Required or Elective: Elective

Specific Outcomes:  In this course, students will:

  1. Learn about biological parts and their properties. Understand gene and enzyme action.
  2. Learn about network structure and pathway engineering.
  3. Understand how synthetic networks can be simulated, built and tested in a real organism.
  4. Learn about manipulating DNA and measuring responses.
  5. Learn how to construct computational models and use them to study network behavior.
  6. Understand the behavior of basic network motifs found in cellular and synthetic systems, including switches, oscillators, filters, logic and pulse devices.
  7. Learn how to build complex modular networks in silico as part of a team project.

Outcomes Addressed by this Course:

This course offers an introduction course on system and synthetic biology. This course is designed for seniors and/or graduates who have an interest in bioengineering at the cellular network level. The first week will include a basic introduction to synthetic biology. The remainder of the course will then cover a variety of more advanced topics.  Students will be introduced to the field of synthetic biology and its application in systems biology and applied engineering. Students will understand in quantitative terms the basic principles of operation of regulation at the cellular level, including metabolic, signaling and gene networks; discover how cellular networks can be reengineered, taking examples from the iGEM competitions and applications such as metabolic engineering; learn how to build computer models of cellular networks; appreciate that cellular systems are very noisy, particularly bacterial systems and how these can be modeled and studied experimentally.  Class assignments are a combination of calculation and computer-based assignments.

As such, this course contributes to the following student learning outcomes:

A. An ability to apply knowledge of mathematics, science, and engineering.

H. The broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context

J. Knowledge of contemporary issues

K. An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice (i.e. computer and analytical equipment)
L. An understanding of biology and physiology.

The knowledge of current synthetic biology topics and practice with synthetic biology techniques imparted through this class contributes to the preparation of our students to reach the Program Educational Objective of earning advanced degrees and/or obtain employment in bioengineering-related fields, such as medicine, device development, or biotechnology and contributing to the responsible development of new technical knowledge.

 Topics Covered:

  1. Metabolic engineering
  2. Case studies of synthetic biology applications
  3. Control engineering theory applied to biology and signaling networks
  4. Cellular regulation (metabolic, signaling, and gene networks)
  5. Computational modeling of cellular networks
  6. Noise in cellular systems

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