Wednesday, March 2, 2016

New Course: EE 426 Synthetic Biology Capstone

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
  1. Proposeformulate and solve open-ended design problems in synthetic biology.
  2. Write formal project reports.
  3. Make formal project presentations.
  4. Work in teams with heterogeneous knowledge and skills.
  5. Apply recombinant DNA methods, gene circuit design, experimental design, and cell-based assays and characterization methods to support design solutions.
  6. Demonstrate an awareness of current issues in and applications of synthetic biology.
  7. Understand the ethics and risks of synthetic biology.
Textbook: Class notes, technical papers and reports.
  1. Writing in the Technical Fields, by Mike Markel, IEEE Publication
  2. Writing Reports to Get Results, by Ron S. Blicq and Lisa A. Moretto, IEEE Publication.
Prerequisites by Topic:
  1. Design and characterization of genetic circuits in bacteria or yeast (for example, EE423).
  2. Design and construction of, and transformation with, recombinant DNA (for example, EE 425).
  3. Computer literacy and experience with synthetic biology CAD tools (for example, CSE 142 for computer programming and EE 425 for CAD tools).
  1. Applications of synthetic biology - 1 week
  2. Project formulation, development of specifications, and background research - 2 weeks
  3. Plasmid and library design and construction - 3 weeks
  4. Construction of transgenic organisms - 2 weeks
  5. Characterization of transgenic organisms using cytometry, microscopy, high throughput sequencing, and/or similar methods – 2 weeks.
  6. 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.
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