Master
Course Syllabus for EE 426 (ABET sheet)
Title: Capstone
Project in Synthetic Biology
Credits: 4
Coordinator: Eric
Klavins, Associate Professor, Electrical Engineering
Goals: This
course provides seniors majoring in the synthetic biology specialty and
practicing engineers with skills in handling open-ended design problems in synthetic
biology. Each student will participate on a team that designs, builds and tests
a new transgenic microorganism with potential applications ranging from
advanced materials, bio-sensing and/or remediation, or human health.
Objectives: At
the end of this course, students will be able to
- Propose, formulate and solve open-ended
design problems in synthetic biology.
- Write formal
project reports.
- Make formal
project presentations.
- Work in
teams with heterogeneous knowledge and skills.
- Apply recombinant
DNA methods, gene circuit design, experimental design, and cell-based
assays and characterization methods to support design solutions.
- Demonstrate an
awareness of current issues in and applications of synthetic biology.
- Understand the ethics and risks of synthetic biology.
Textbook: Class
notes, technical papers and reports.
References:
- Writing
in the Technical Fields, by Mike Markel, IEEE
Publication
- Writing
Reports to Get Results, by Ron S. Blicq and
Lisa A. Moretto, IEEE Publication.
Prerequisites
by Topic:
- Design
and characterization of genetic circuits in bacteria or yeast (for
example, EE423).
- Design
and construction of, and transformation with, recombinant DNA (for
example, EE 425).
- Computer
literacy and experience with synthetic biology CAD tools (for example, CSE
142 for computer programming and EE 425 for CAD tools).
Topics:
- Applications
of synthetic biology - 1 week
- Project
formulation, development of specifications, and background research - 2
weeks
- Plasmid
and library design and construction - 3 weeks
- Construction
of transgenic organisms - 2 weeks
- Characterization
of transgenic organisms using cytometry, microscopy, high throughput sequencing,
and/or similar methods – 2 weeks.
- Final
presentations – 1 week.
Course
Structure: The class meets for two lectures a week, each consisting of a
50-minute session, and two lab sessions each week, each consisting of a 50
minute session. Students work in teams or two or three, and are expected to
meet outside of class as necessary to set up their experiments, monitor
progress, and complete their project. There will be weekly design review presentations
involving the entire class, and seminars on relevant topics during scheduled meeting
times. Students should keep detailed electronic laboratory notebooks. A written
and oral project report from each team will be presented during finals week.
Computer
Resources: Students will make use of the Aquarium Lab OS, CAD tools
such as Coral or Benchling, laboratory instrumentation and control software, and
analytical software such as MATLAB, R, and Python.
Grading: Project work accounts
for the vast majority of the course grade. Teamwork as well as individual
performance will be assessed.
Laboratory
Resources: Students will use the UW Biofab to build their organisms and
to implement their experiments. They may also perform bench work in the labs of
participating faculty.
Outcome
Coverage: This course provides the ABET major design experience and
addresses all of the basic ABET outcomes.
Outcomes:
A.
(M) an ability to apply knowledge of mathematics, science, and
engineering. The design of synthetic gene networks demands constant
use of knowledge of mathematics, science and engineering. The behavior of
various genes and networks in governed by biology and chemistry, modeling using
ODEs, and is best-understood using statistics. The design of a system to a
given set of objectives is a fundamental application of engineering knowledge.
Thus, a successful design shows the student's achievement of this outcome.
B.
(M) an ability to design and conduct experiments, as well as to analyze
and interpret data. Students will develop experiments and controls to
refute hypotheses about how their transgenic organisms will behave. In
addition, debugging the design and construction of DNA affords many
opportunities to apply the scientific method.
C.
(H) an ability to design a system, component, or process to meet
desired needs within realistic constraints such as economic, environmental,
social, political, ethical, health and safety, manufacturability, and
sustainability. The students will develop specifications defining the desired
behavior of a transgenic organism for an information processing, advanced
materials, or human health application. Students must choose among design
alternatives on the basis of economic costs versus environmental, social,
ethical, and political considerations. A discussion of environmental impacts
and mitigation plans is required in the final project report.
D.
(H) an ability to function on multi-disciplinary teams. Students
operate in teams of two or three to solve the design problem and prepare a
final report. Students will take different roles in the design team, such as
leader, explorer, reflector, or recorder. Rotating leadership is recorded on assignments
and progress reports. Teams will collaborate with graduate student and
postdoctoral scholar advisors from labs around campus, and will learn how to
translate ideas from engineering to biology and vice verse.
E.
(M) an ability to identify, formulate, and solve engineering problems. The
design problem presents itself as a series of interconnected engineering
problems. In the open-ended design environment, the engineering problems are
not explicitly stated, but must be identified by the design team before they
can be solved. Evidence of this should appear in the project report and design
reviews.
F.
(L) an understanding of professional and ethical responsibility. At
least one entire lecture will focus on ethics and another on biosafety.
Students will be required to address each of these subjects in their project
reports.
G.
(H) an ability to communicate effectively. Teams must prepare presentations
for each design review, keep detailed lab notebooks, and solve problems in
scrum style meetings with their teammates. Each team member must write a
section of their final report, and team members must prepare part of the
presentation. Grades are given for writing quality and presentation quality, as
well as technical content of the reports.
H.
(M) the broad education necessary to understand the impact of
engineering solutions in a global, economic, environmental, and societal
context. In seminars, various social impacts and applications of synthetic
biology are discussed and described, ranging from understanding the economics
of materials synthesis, diagnostics in third world settings, to gene therapies.
Constraints on the projects include environmental and social concerns. Discussions
will be facilitated among the students on these topics in preparation for
various design reviews and final reports.
I. (M) a
recognition of the need for, and an ability to engage in life-long learning. The
course material distributed will not contain all of the information necessary
to solve the design problem. Students must work with graduate student and
postdoctoral methods, consult reference sources, and inform themselves
concerning many aspects of their design problem. This helps students realize
that they need to be able to learn material on their own, and gives them some
of the necessary skills.
J.
(H) a knowledge of contemporary issues. The design problem is
constructed to focus attention on current applications of synthetic biology in
industry and medicine such as the issues surrounding GMOs, the ethics of
cloning and gene therapy, environmental containment, and intellectual property.
These ideas and more should appear in the project reports. In addition,
seminars by guest speakers later in the class will address current issues in
synthetic biology.
K.
(M) an ability to use the techniques, skills, and modern engineering
tools necessary for engineering practice. Students are expected to use
computer aided design tools, laboratory automation software, version control
software, and mathematical software to design, plan, and evaluate the systems
they build. Evidence of the use of these tools, and associated techniques,
appears in the project report.
Preparer: E.
Klavins
Last
revised: Dec 7, 2015
