Current Teaching

2019 Introduction to Synthetic Biology Syllabus

BIOEN 423/523, CHEME 498/599, CSE 486/586, EE423/523, MOLENG 525

Credits: 3

Lecture: MWF 12:30-1:20, PCAR 290

Instructors:

Prof. James Carothers, jcaroth@uw.edu

Prof. Georg Seelig, gseelig@uw.edu

Synthetic biology is an emerging discipline focused on engineering biological parts and systems for applications in Materials, Chemicals, Energy, the Environment, and Health. Synthetic biology involves engineering genetic regulatory mechanisms and networks, signaling pathways, metabolisms, and biomolecules such as proteins and nucleic acids. Applications include new tools to study biological systems, novel diagnostics and therapeutics, bio-based platforms for chemical and material synthesis, and engineered cells and strains for industrial processes.

UW Catalog Description:

Mathematical modeling of transcription, translation, regulation, and metabolism in the cell; computer-aided design methods for synthetic biology; implementation of information processing, Boolean logic and feedback control laws with genetic regulatory networks; modularity, impedance matching, isolation and integration in biochemical circuits; and parameter estimation methods.

Specific course outcomes:

By the end of the course you should be able to:

1) Use mass action kinetics and chemical reaction networks to model biochemical reaction networks and gene regulatory networks.

2) Write code in Python to simulate deterministic chemical reaction networks.

3) Design and model the behavior of simple genetic circuits and metabolic pathways.

4) Discuss and think critically about scientific papers in synthetic biology.

5) Discuss and think critically about ethical issues in synthetic biology.

Progress in learning the material is measured with weekly homeworks and two in-class exams.

Prerequisites by Course: Either MATH 136 or MATH 307, AMATH 351, or CSE 321 and MATH 308 or AMATH 352.

Prerequisites by Topic:

Elementary differential equations and applications, linear algebra and numerical analysis, basic computer programming. No prior knowledge of biology beyond high school is needed.