To empower young scientists to shape synthetic biology, the Hopkins iGEM team developed a course, EN.580.150 Synthetic Biology Design. This course was designed to introduce freshmen to concepts in synthetic biology over a 3 week period during winter between semesters. The course was open to all undergraduate students at Johns Hopkins University and had ten enrollees who had little or no familiarity with synthetic biology. From the success of this course we hosted in January, a few of the students joined the 2023 Hopkins iGEM team.


Synthetic biology is the practice of re-engineering organisms to perform a useful task. In this course, students will be exposed to the relatively novel field of synthetic biology through lectures and activities on

  1. genetic design techniques and tools for DNA assembly
  2. hardware designs for biological measurement
  3. ethics, safety, and security concerns regarding bioengineering and
  4. mathematical modeling of genetic circuits.

Students will present a project at the end of this course synthesizing everything they have learned.


By the end of this course students should be able to:

  • Identify appropriate procedures for assembling, cloning, and isolating plasmid DNA
  • Assemble the electronic hardware for a photometer to measure bacterial cultures
  • Discuss ethical issues in synthetic biology and current solutions for biosecurity and safety
  • Utilize computational platforms for modeling biological systems


Student members of the iGEM team were instructors. They developed all lecture materials and in class activities and delivered the lessons for each of the different modules.

  • Wetlab Instructor: Sreenivas Eadara
  • Hardware Instructors: James Li
  • Human Practices Instructor: Siyona Mishra
  • Mathematical Modeling Instructors: Tiara Safaei, Josh Devier


The course met thirteen times with class duration of 1 hour and 40 minutes. The classes were held hybrid with students joining in-person in a classroom or lab or synchronously online on Zoom.


Wetlab Module

Through lectures, students learned about DNA assembly. Through lab activities, in groups they chose their own chromoprotein and then followed protocols to assemble it into a plasmid and transform the plasmid into E. coli.

  1. Lecture on DNA Assembly Introduction
  2. Lecture on Fluorescent Proteins & Chromoproteins
    1. Protocol: Assembly with BsaI
  3. Lecture on Transformation and Plasmid Design
    1. Protocol: Transformation
  4. Lecture on Introduction to Final Project
    1. Protocol: Colony Selection
  5. Protocol: Miniprep
  6. Wetlab End of Module Exercise

Hardware Module

Through lectures, students learned about computer aided design and basics of electronics. Through lab activities, they made designs to be 3D printed and then assembled the electrical components of a photometer to measure the fluorescence and optical density of the bacterial cultures they engineered to express a chromoprotein.

  1. Lecture on Introduction to Hardware - Mechanical
    1. Protocol: 3D Printing
  2. Lecture on Introduction to Hardware - Electrical
    1. Protocol: Photometer Assembly
  3. Hardware End of Module Exercise

Human Practices Module

Through lectures, students learned the history of synthetic biology, guiding principles of the field, ethical concerns, and risk reduction strategies. As an end of module exercise, students were asked to have dialogues about case studies of historical ethical dilemmas in synthetic biology.

  1. Lecture on Synthetic Biology Ethics

Math Modeling Module

Through lectures, students learned about the fundamentals of building models from processes to differential equations and about different kinds of biological controls that can be modeled. For in-class exercise, students practiced using SimBio to model systems like gene regulation pathways. Additionally, students had a lecture on macromolecular structure and the types of simulations that are available for folding these structures. As a in-class exercise, students used a software to fold a macromolecule of their choice (eg. SAR-CoV-2 spike protein 1, Insulin, or Ion Channel) and presented their findings to the class.

  1. Lecture on Biological Circuit Modeling
    1. SimBiology Model Exercise
  2. Lecture on Protein/Nucleic Acid Folding + Design


Students used the techniques they learned in the lectures and practiced through the exercises to complete a final project. For the project, students identified a problem that can be addressed with bioengineering, conceptualized a potential solution, presented their ideas in a 15 minute presentation, and provided feedback to peers.


Class attendance was recorded and contributed toward the course grading. By attending the classes either in-person or virtually, students were introduced to all the concepts needed to sufficiently complete exercises. Furthermore, in both modalities, students were able to collaborate with peers as well as receive immediate feedback on class exercises and the final project from the instructors during class time. However, students attending in-person had the opportunity to participate in more hands-on activities such as executing protocols in the laboratory.

Attendance was recorded through exit surveys.

Example of exit survey questions:

  • Rank how familiar you were with today's material before the class
  • Rank how did you find the presentation
  • How familiar were you with today's protocol before the class?
  • Rank how did you find the experience of executing the protocol
  • Rank how did you find the class today
  • What is one takeaway from today?
  • What questions do you have from today?
  • Any other questions/comments/concerns about the course overall?


The course had four module exercises (each worth 15%) and one project (worth 30%) which were graded for completion. The final 10% of the grade was from attendance. The course was graded as Satisfactory/Unsatisfactory since it was an Intersession course, with Satisfactory earned by 70%+.


At the end, the students in the class submitted evaluations of the course through a survey designed by the university to compare all courses equally. This Synthetic Biology Design course scored on par with the mean scores of courses in the department and at the university.

  • The overall quality of this course was reported as good (78%) and excellent (22%).
  • The instructors’ teaching effectiveness was reported as good (33%) and excellent (67%).
  • The intellectual challenge of this course was reported as satisfactory (11%), good (44%), and excellent (11%).

Excerpts from open response questions:

What are the best aspects of this course?

  • "I have really solidified my knowledge on synthetic biology, and I have also learned many new things (3D printing, electrical circuits, biological modeling and mathematical model via Matlab, etc.) The class has also helped me to make substantial progress on a research project I have also been attempting to develop! I will definitely recommend this course to others if it is still being offered next year!"
  • "variety of interesting topics and applications covered, hands-on lab opportunities"
  • "Going over various methods, models, and hand-on topics that were very informative."
  • "The ideas that were covered were very interesting especially the module about bioweapons and biological circuit modeling."
  • "It seemed that the instructors were very knowledge on the concepts of synthetic biology. Whenever students had questions they received well-though out answers that often pulled on real-world examples of applications of the concepts we were discussing in class."
  • "I got to learn some cool stuff"
  • "I enjoyed every part of the class"

What are the worst aspects of this course?

  • "difficult to follow along without previous background in material"
  • "None"
  • "There is a steep learning curve to some of the concepts discussed and a lot of assumed knowledge we're expected to have."
  • "I feel that the lectures could have been better targeted for the inconsistent background level of the students."
  • "I cant think of anything"

What would most improve this class?

  • "None"
  • "I believe that it would have been better if it was anticipated that students would not have background knowledge on topics like electronics. The other approach would be to state what the expectations were somewhere, but I don't think that would be the best option as it's meant to be an overview so I think it's most valuable if the class is easily accessible."
  • "I cant think of anything"
  • "The lectures tend to quite long and may be draining decreasing the attention span of students."

What should prospective students know about this course before enrolling?

  • "Having some background knowledge in biology/wet lab & dry lab skills in general will help you to follow the pace of the course better"
  • "Maybe some basic biology and physics concept(electricity)"
  • "Its a fun class"
  • "Be prepared to explore and don't be afraid to hit a dead end"