Duke Biomedical Engineering

BME 406L/706L: Biotechnology Design II

Course syllabus. This page updates from the syllabus document every day.

BME 406 Syllabus

Course Overview

What is this course about? This course, a continuation of BME405L/705L: Biotechnology Design I, focuses on implementing group-based research projects. These projects are derived from designs conceptualized in the previous semester and are refined in consultation with the instructional team and supporting faculty.

Key elements of the course include:

  • Laboratory Practicals: Students will engage in hands-on laboratory work to create an initial proof of concept or prototype for a biotechnological product or process.
  • Lectures: Supplemental lectures will cover project design, ethical considerations in biotechnology, regulatory and stakeholder analysis, and intellectual property rights.
  • Final Deliverables: A comprehensive final report and a poster presentation, targeting both technical and general audiences, will conclude the course.

Background Knowledge

What should I know before taking this course?

Prerequisites

  • Mandatory Course: Completion of Biotechnology Design I (BME405).
  • Core Knowledge Areas:
  • Molecular and Cell Biology (e.g., Biology 201/203L)
  • Quantitative Modeling/Data Analysis (Excel, Matlab, Python, and/or R)
  • Human Physiology (BME 244L)
  • Molecular/Cellular Engineering (BME305L/306L)
  • Transport Phenomena (BME 307)

Additional Requirements

  • Literature Analysis: Students should be adept in analyzing primary research and review articles.
  • Presentation Skills: Proficiency in written and oral presentations is essential.

Course Objectives

What will I learn in this course?

In this course, you will engage actively and upon successful completion, you will:

  1. Implement the Engineering Cycle: Apply the design-build-test-learn cycle independently and in groups to develop biotechnological advances.
  2. Explore Biotechnologies: Delve into modern biotechnologies through primary literature and interactions with stakeholders and industry leaders.
  3. Laboratory Skills & Quantitative Analysis: Develop laboratory skills and perform quantitative analyses aligned with current practices in biotechnology and bioengineering.
  4. Communication Skills: Effectively communicate scientific data, experiments, and designs to various audiences in both oral and written formats, individually and as part of a team.
  5. Ethical Research Conduct: Conduct research responsibly with accurate documentation and address ethical dilemmas associated with biotechnology research.

Course Outcomes

What should I be able to do after completing this course?

After completing this course, you should be able to:

  1. Literature Analysis: Analyze primary literature, protocols, and perspectives to advance novel biotechnologies in and beyond the laboratory.
  2. Strategic Planning: Develop and execute strategic plans for future biotechnology products or advances, adhering to the design-build-test-learn cycle.
  3. Stakeholder and Market Analysis: Identify and understand the role of critical stakeholders, market factors, and regulatory practices in biotechnology design.
  4. Master advanced Laboratory Techniques: as part of laboratory exercises and design implementation you will learn methods such as: cell culture, DNA delivery, kinetics and binding assays, quantitative gene expression, assay development
  5. Quality control Data Analysis and Hypothesis Testing: Measure biological data and perform statistical analyses to validate or refute scientific hypotheses related to project designs.
  6. Effective Presentation: Present biotechnology arguments and designs to scientific and general audiences in various formats, including pitch talks, poster presentations, and manuscripts.
  7. Team Collaboration: Work effectively and collaboratively within an engineering team.

Course Structure

What will I do in this course?This course, BME 406L/706L, is the second semester of a two-semester design sequence for BME seniors. Following Biotechnology Design I in the fall, this spring semester course counts as the BME design course, building upon the advanced BME elective in molecular and cellular engineering (MC).

Lectures

  • Content: Lectures will cover historical and current biotechnological advances through instructor-led sessions, guest lectures, team activities, and student presentations.
  • Participation: Active participation in discussions is crucial for understanding the design process. We will also use lectures for project check-ins, feedback, and collaborative activities.
  • Attendance: Regular attendance is vital. Please inform Dr. Chory of any planned absences.

Laboratory Practicals

  • Initial Phase: Before receiving project materials, students will engage in laboratory practicals covering essential biotechnology design exercises and quantitative data analysis.
  • Lab Practicals: Each student must complete two (2) out of five (5) available lab practicals, ideally choosing those relevant to their team’s design.
  • Deadlines: All lab practicals must be completed before spring break (March 8-March 18).

Lab Documentation and Data Management

In this crucial component of the course, students will engage in comprehensive digital documentation and management of lab data, primarily utilizing the Benchling platform including:

  • Electronic Lab Notebook: Students must maintain an electronic lab notebook in the BME406 Benchling group documenting experiments, assay designs, and data, with instructional guidance provided.
  • Data Organization & Analysis: Mastering data management skills including organization, analysis, and visualization within a digital framework.
  • DNA Sequence Design: Implementing sequence alignment, annotation, and manipulation techniques using Benchling and/or Geneious, to proficiently design and analyze DNA sequences for various applications.

Additional for Master’s Students (BME706L): For master’s students enrolled in BME706L, there will be an additional assignment to differentiate between the undergraduate and the graduate version of this course. This will be assigned as a prepared chalk talk on an ongoing project or a new project that extends from the design project.

Grading

How will my grade be determined?

The following table lists the assignments and their weight in the overall grade:

Grading CategoryLearning ObjectivesGrade %Ownership
Lab Citizenship & Peer Evaluation*3, 4, 515%Individual Grade
Laboratory Practicals (2)2, 3, 410%
Participation/Communication (Slack)3, 4, 515%
Laboratory Notebook (5-10 checks)3, 4, 55%Group Grade
Weekly Check-in Meetings/Progress Reports1, 3, 4, 55%
Mid-semester Progress Presentation1, 3, 410%Group Grade
Final Design Poster and Presentation (oral)2, 3, 510%
Drafts + Final Design Manuscript (written)1, 2, 3, 4, 530%
Total100%

Note: If you are enrolled in BME706L, you must also submit an additional assignment. This will be a chalk talk presented during the final exam period (5 May 9am-12pm). This adjusts your final grade breakdown with your Final Design Report to 20% and your Grant Report for 10%

This course is not “curved” (i.e., a distribution of grades will not be enforced), and a traditional grading scheme will be used (e.g., 90-93.00 = A-, 93.01-97.00 = A, 97.01-100 = A+). All grades will be posted to Canvas throughout the semester to track your performance. Any re-grading requests need to be made within one week of grades for a given assignment being returned, with a description of why you feel a re-grade is appropriate.

Group Grades

As a continuation of the Biotechnology Design sequence, this course focuses on the implementation of independently proposed design projects from the previous semester. Students will engage in hands-on lab work, culminating in a series of evaluations that reflect their progress and mastery of biotechnological design principles. This semester is dedicated to bringing your proposed design projects to life. The following components will constitute the core of your grade, reflecting the diverse aspects of project development from concept to presentation.

Weekly Check-in Meetings & Progress Reports (5%)

  • Teams will have weekly 30-minute 1:1 meetings (sign up form link) with the instructional team to discuss progress, timelines, and to review lab notebooks for grading.
  • Assessment: Based on project updates, teamwork, and preparedness for final deliverables.

Lab Notebooks (5%)

  • Lab notebooks will be graded for thoroughness and clarity. Proper documentation is essential to reflect the progress and reproducibility of your work.
  • Assessment: Comprehensiveness of experimental details are comprehensive, figures are well-labeled and clear, and protocols and observations are meticulously recorded.

Lab Meeting Presentation

  • Early in the semester, each team will give a single 10-minute presentation during a lab meeting to update the class on their project. The presentation is meant to be informal, with time for 3-5 minutes of questions and feedback from peers.

Mid-Semester Progress Report & Presentation (10%)

  • Presentation: A formal presentation showcasing initial results, challenges, and revised design approaches.
  • Report: Teams will also submit a revised design report to be graded via peer assessment.

Final Design Poster and Presentation (10%)

Project teams will present at the BME Design Symposium (Date TBD) and share a poster and a two-minute pitch video on their proposed design and results. More information will be provided as we approach this date, but weekly progress meetings will practice these oral and written skills.

Final Design Manuscript (30%)

A comprehensive final design report will be required that shares your findings and results from the semester. This will be written in manuscript format (abstract, introduction, results, discussion, materials and methods, etc.) in combination with your initial proposal report (stakeholder analysis, IP and regulatory findings). 10% of this grade will be allocated to progress reports compiled throughout the semester. These reports will consist of key sections of the manuscript (e.g., introduction, methods, results) and a manuscript/storyboard outline of the final design manuscript. These incremental submissions will ensure teams are building their final deliverable in a structured and systematic manner.

Individual Grades

Lab Citizenship & Peer Evaluation (15%)

This category evaluates your contribution to a respectful, safe, and well-organized lab environment. Key elements include proper equipment usage, maintaining a clean workspace, adhering to safety protocols, and respectful communication with peers and staff. Your peers will also assess your teamwork and collaboration. These behaviors ensure an efficient and professional atmosphere, crucial for a productive lab experience and your future career. For more details, see the section below on Lab Citizenship.

Your adherence to these principles of lab citizenship accounts for a substantial portion of your course grade, emphasizing their significance in our teaching lab environment. This policy aims to recognize and promote behaviors that contribute to a positive, efficient, and professional atmosphere in the lab. By meeting these standards, you excel in this course and build a strong foundation for your future career in biotechnology and related fields.

Laboratory Practicals (2) (10%)

You will complete two hands-on laboratory practicals designed to assess your technical skills and understanding of key lab techniques. These exercises simulate real-world lab scenarios, evaluating your ability to follow protocols, troubleshoot issues, and generate high-quality data. The practicals provide an opportunity to demonstrate mastery of essential biotechnology techniques.

  • Deadlines: All lab practicals must be completed before spring break.

Participation/Communication (Slack) (15%)

Effective communication is critical to the success of your projects and your professional development. Teams that actively use Slack for scheduling, project updates, sharing data, collaborative problem-solving, and even resolving disputes consistently achieve better outcomes. By participating on Slack, you’re not only contributing to your team’s success but also developing a highly transferable skill. Slack is widely used in academia and industry as a primary communication tool, and proficiency with it will be valuable for any career path you choose. This category evaluates your timely and professional use of Slack to stay engaged, share progress, and collaborate effectively with teammates, TAs, and instructors. Active and organized communication ensures a smooth workflow and a supportive, productive learning environment.

IMPORTANT:We highly discourage communication on other platforms for project-related discussions (i.e. iMessage, Whatsapp, private DMs). As an example, Professor Chory, who is a Venture Partner with a venture capital fund, signed an agreement requiring that professional communication must remain on official channels such as Slack and email. The agreement stated:

"The Parties agree that private and professional communication channels must always be kept separate. Furthermore, to clarify future communication methods, only the channels 'Email' and 'Slack' will be used, to facilitate smooth project execution."

This reflects industry standards and underscores the importance of keeping discussions centralized, professional, and well-documented. For more details, see the section below on communication expectations.

Course Expectations

What should I know about this class to prepare for success?

Expected Individual Workload

Independent design projects require a significant amount of time and project management, especially as the majority of class time will be spent outside of formal lectures. Communication is essential to your success in this class—with your teammates and instructional staff. We will assist with purchasing materials, providing protocols, and other support for in-lab hours. We will discuss project management tools and lab notebook reporting in the first two weeks to prepare you for success. Aim for approximately 5-10 hours per week, with additional time during crucial phases (e.g., final poster, presentation).

Attendance

We know that students may be preparing graduate school/medical school interviews, internships, recruitment, job interviews, and fellowships during this year. Lecture attendance and laboratory participation will be expected unless there are extenuating circumstances. Flexibility with Notice: If you have an immovable conflict, please provide ample lead time for any scheduling conflicts; we'll work to find solutions. Last-minute notices will limit our ability to accommodate. While we can’t bend the rules and procedures every week, we can work together to come up with solutions when necessary.

Research Integrity

Honesty, transparency, and integrity are fundamental to our teaching lab culture. Your work should be original, and all collaborative efforts must be properly credited. These principles are not merely guidelines but essential skills that prepare you for the realities of professional lab work.

Lab Citizenship

Respect & Laboratory Stewardship

  • Considerate Resource and Equipment Usage: Return all equipment, pipettes, and reagents to their rightful places after use, and handle them with care, acknowledging that these are communal resources.
  • Respect for Others: Be mindful of your peers and shared spaces. Minimize disruptions and share resources fairly.

Clean and Organized Lab Space

  • Tidy Workspace: Keep your area clean and organized. This includes proper waste disposal, reagent storage, and an accessible space.
  • Waste Management Diligence: Properly dispose of waste materials and be vigilant about waste bin levels, replacing them when full to maintain a clean lab environment.
  • Collective Effort: Everyone's participation is crucial in maintaining a clean & safe teaching lab.

Safety & Incidents

  • Prompt Incident Reporting: It is essential to immediately report any equipment malfunctions, accidents, or safety concerns. We understand that accidents happen and equipment can fail. These incidents are a natural part of the learning and research process.
  • Safety First: Your safety and the well-being of others is our top priority. Your grade will never be penalized for reporting lab accidents or research mistakes. In fact, acknowledging and learning from these incidents is a valuable part of your training.
  • Consequences of Non-Reporting: Failing to report incidents can have more significant negative consequences than the incidents themselves. Timely reporting helps us address issues promptly and maintain a safe and productive lab environment for everyone.

Time-management and respectful communication

Our Teaching Assistants (TAs) and lab staff are dedicated to supporting your learning and project success. It is essential to respect their time and boundaries. This means:

  • Communication Hours: Please attempt to communicate with TAs and lab staff during reasonable hours, typically between 9 AM and 6 PM on weekdays. Avoid sending messages outside these times unless it is a real emergency.
  • Understanding Emergencies: A real emergency is an unexpected and serious situation requiring immediate action, such as a safety concern in the lab. A project urgency, while important, does not constitute an emergency. As such, please only reach out to the lab emergency contacts in the event of a real emergency, and use Slack to communicate with TAs about other concerns or project urgencies.
  • Scheduled Meetings: Honor your scheduled meetings with TAs and lab instructors. These are valuable opportunities for guidance and feedback. If you must cancel, do so with advance notice and reschedule promptly.
  • Slack/Email Etiquette: When emailing TAs or lab staff, be concise and professional. Include relevant course and team details to help address your concerns efficiently.

Lab Logistics

Lab Space Availability & Resources

  • Rooms P05/P04 - This is the primary student workspace equipped with a broad range of equipment necessary for various biotechnology projects. It offers flexibility for students to start cultures or carry out other tasks even during scheduled lab sessions.
  • Room P03a- Home to the flow cytometer and the gel imager. The flow cytometer is available by booking only using this reservation link.
  • Room P011 - Contains supplementary equipment. Most students might not require the use of this room, but it is available should the need arise.
  • Rooms P012 & P015 - These rooms are dedicated to mammalian cell culture, each featuring CO2 incubators and necessary associated equipment for cell maintenance. P012 is outfitted with two Biosafety Cabinets (BSCs) and numerous microscopes, while P015 has several BSCs for student use.

Time Restrictions

Please note the following times when the rooms are reserved for specific classes and unavailable for general use:

  • Thursdays 10:00 AM - 9:00 PM Teer P015, P012 reserved for BME306
  • Fridays 1:00 PM - 6:00 PM Teer PO5 reserved for BME564

Students are encouraged to schedule their lab time around these classes and book equipment in advance where necessary.

Ordering Lab Materials

  • Placing Orders: After the initial orders (placed in Biotech Design I), you may require additional reagents for your projects. To place these orders, please use this Order Request Form, and we will place the orders on your behalf.
  • Budget Allocation: Each group has approximately $2000 for reagents this semester, excluding common consumables like plastics and media.
  • Spending Monitoring: Keep track of your group's expenditures using this Budget Tracker.
  • Cost Awareness: Gaining familiarity with the costs of lab materials is crucial for those aspiring to manage a startup, research lab, or any scientific endeavor. It develops financial acumen and resource management skills, key competencies for successful leadership in these areas.

Communication Expectations

BME406L offers a unique and independent laboratory experience, largely thanks to the flexibility and dedication of our TAs and lab staff. Compared to other courses where TAs have highly structured obligations (set office hours, weekly homework assignments, etc), our TAs are required to be more adaptable, offering flexible support across various activities and projects. Although they are exceptionally committed, it's important to understand that they cannot provide immediate, round-the-clock assistance due to their own research and teaching responsibilities. To balance this, we are trying out a new, structured yet flexible communication system, which is detailed below:

Slack will be our primary mode of communication. Announcements, updates, and direct messages will all take place on Slack. It is essential that you check Slack regularly to stay informed about any announcements, lab updates, direct messages from peers/instructors, etc. We encourage you to download both the desktop and phone app for best use.

Grades and formal assessments will be posted on Canvas. Please ensure you are familiar with navigating Canvas to access your grades and course materials.

General Lab-related Queries

TAs “On-call

For general lab questions like cloning techniques, equipment operation, or protocol doubts, TAs and Instructors will be available during specific 'on-call' hours, available via slack, or in the lab, upon request. This system ensures that you get help quickly, especially for general lab inquiries or urgent issues, from either your classmates, the TAs, or instructors. It also allows for better utilization of TA availability, ensuring that someone knowledgeable is always at hand to assist you. Balanced Workload: This helps in managing the TAs' workload, ensuring they can provide quality assistance without being stretched too thin. Remember, even if the “on-call” TA is not your assigned project, all TAs and staff are equipped to provide in depth guidance in the lab.

Availability

The general availability of each of the TAs will be posted as a “pinned” message in the #help-desk slack channel.

Planning for Direct Assistance

If you anticipate needing in-depth TA support, communicate in advance using your team-specific Slack channel. While TAs are committed to supporting your learning, they have other responsibilities as well. They will respond as promptly as possible, but there might be occasional delays (they have on-going experiments too!).

Project-specific feedback

Dedicated TA

Every group will have a dedicated TA who has specialized knowledge of their project. Each group will then also have a private Slack channel with their TA and Dr. Chory or Dr. Kim for in-depth project discussions and scheduling meetings.

Advance Scheduling:

Use your project-specific Slack channel to schedule meetings with your assigned TA. We encourage you to arrange these meetings during their designated on-call hours when possible. If your assigned TA’s on-call hours don’t align with your schedule, you can still request a meeting outside these hours. However, please do so well in advance.

Direct Messages

Students can use DMs for private conversations or sensitive matters with their TAs or professors.

Slack channels

  • #bulletin-board - For general announcements, updates, reminders, etc.
  • #help-desk - For support and office-hours-like questions from peers, TAs, or instructors.
  • #lab-practicals - For discussions, questions, and coordination on lab practicals.
  • #yer-a-data-wizard - For discussions on quantitative data analysis and statistical methods.
  • #design-lounge - This Channel is for sharing fun science finds, campus events, memes, etc.
  • #red-alert-zone – This channel is reserved for lab issues, broken equipment, and true emergencies. Please only post to the channel if you need immediate assistance.

Communication Etiquette

Response Time

Students should anticipate varied response times, as TAs will prioritize questions asked during on-call hours.

Professional Standards

Whether posting in general or group-specific channels, students should maintain professionalism and courtesy. Be punctual and prepared for scheduled meetings, respecting the TAs' time and other commitments.

Feedback and System Adjustments:

We regularly seek feedback to ensure the communication system meets the needs of both students and teaching staff. Necessary adjustments will be made to enhance efficiency and responsiveness. If you have any concerns with the communications system, please use this Qualtrics survey to provide anonymous feedback, or send a direct message to Dr. Chory or Dr. Kim.

Course Policies

Course Materials

What required texts, materials, and technologies will I need?

We will use Slack, Benchling, and Canvas to share lecture notes, laboratory protocols, and other resources. You will also submit all assignments via Canvas for ease of use and a centralized location. Papers, videos, and other excerpts from literature will be provided on Slack, but you may also need the Duke Library website or databases (e.g. PubMed, Google Scholar) to find additional resources for the class, especially when preparing your design proposals.

What optional texts or resources might be helpful?

There are no required textbooks for this class, but there are many reference and supporting texts that may be useful for your design proposals and future research endeavors. The NCBI Bookshelf offers many older editions of these books or similar references online for free. Please reach out to Dr. Chory if you would like any supplemental reference texts beyond this list:

Academic Integrity

As a student, you should abide by the academic honesty standard of the Duke University. Its Community Standard states: Duke University is a community dedicated to scholarship, leadership, and service and to the principles of honesty, fairness, respect, and accountability. Citizens of this community commit to reflect upon and uphold these principles in all academic and nonacademic endeavors, and to protect and promote a culture of integrity.

To uphold the Duke Community Standard:

  • I will not lie, cheat, or steal in my academic endeavors;
  • I will conduct myself honorably in all my endeavors; and
  • I will act if the Standard is compromised.

Academic Policy & Procedures

You are responsible for knowing and adhering to academic policy and procedures as published by the Office of Student Conduct. Please note, an incident of behavioral infraction or academic dishonesty (cheating on a test, plagiarizing, etc.) will result in immediate action from me, in consultation with university administration (e.g., Dean of Undergraduate Studies, Student Conduct, Academic Advising).

Academic Accommodations

If you need to request accommodation for a disability, you need to contact the disabilities management office. I will work with that office to provide you with equal access to course materials and make accommodations for exams and other assessments.

Respect for all students

It is our intent that students from all backgrounds and perspectives be well served by this course, that students' learning needs be addressed both in and out of class, and that the experiences and perspectives students bring to this class be viewed as a resource, strength, and benefit. It is our intent to present materials and activities that are respectful of all students, regardless of gender, sexuality, disability, age, socioeconomic status, ethnicity, race, or culture. Your suggestions are encouraged and appreciated. Please let us know ways to improve the effectiveness of the course for you personally or for other students or student groups. In addition, if any of our class meetings conflict with your religious events, please let me know so that we can make arrangements for you.

Providing Feedback

You are invited to provide feedback on this course, either anonymously or directly to instruction staff. Our emails are provided or you can email us to request a one-on-one meeting. Please allow us 24 hours to respond to your email. If you wish to provide anonymous feedback, you may use this Qualtrics survey. This feedback form is reviewed as comments come in.

AI Policy for BME59011Adapted from Prof. Aaron Kyle’s AI Policy for BME 473

The utilization of AI tools will be beneficial for BME590. You are permitted to use AI for code on your final projects, but you are not encouraged nor permitted to use it for code in the bootcamps. The bootcamps exist so that you learn the process and work through the assignments yourself.

When you do use AI, please be sure to consider the following:

  1. Transparency & Disclosure: Identify where and how you have used AI, including an explicit statement of what tool was used and the prompts you used.
  2. Verification: Recover the sources that gave rise to the AI outputs to ensure that the outputs are rooted in real work.
  3. Attribution:Cite the original work that gave rise to the output. AI is not a primary source.

For the final project, submit your prompts as an appendix to your code (an AI_USE.md file in your repository). For the bootcamps, you may ask AI to explain a concept, an API, or an error message you have already read, but list those prompts at the top of the notebook. Code that you did not write yourself does not count as your work.

You are encouraged to use the engineering design framework in which you consider AI a Tool, a Teammate, or Neither (further details can be found in Willems et al.)

TOOLUse AI for repetitive tasks to enhance overall team outputImprove efficiency and efficacyAssist with acquiring and synthesizing new knowledge
TEAMMATECritically review materials that you develop (editorial review)Complement or augment your innovation outputs
NEITHERNot using AI to replace human-driven activitiesThe bootcamp exercises, where you learn the processBuilding, testing, iteration

Additional University Resources

What university resources can help me during this course?

Academic Advising and Student Support

Please consult with me about appropriate course preparation and readiness strategies, as needed. The Academic Resource Center (ARC) offers free services to all students (e.g., peer tutoring, learning consultations, ADHD/LD coaching, and help with online learning.

Consult your academic advisors on course performance (i.e., poor grades) and academic decisions (e.g., course changes, incompletes, withdrawals) to ensure you stay on track with degree and graduation requirements. Please speak with the Academic Advising Center for additional support.

Mental Health and Wellness Support

Student mental health and wellness is of primary importance at Duke, and the university offers resources to support students in managing daily stress and self-care. Duke offers several resources for students to seek assistance on coursework and to nurture daily habits that support overall well-being, some of which are listed below:

If your mental health concerns and/or stressful events negatively affect your daily emotional state, academic performance, or ability to participate in your daily activities, many resources are available to help you through difficult times. Duke encourages all students to access these resources.

  • DukeReach:Provides comprehensive outreach services to identify and support students in managing all aspects of well-being. If you have concerns about a student's behavior or health visit the website for resources and assistance. http://studentaffairs.duke.edu/dukereach
  • Counseling and Psychological Services (CAPS): CAPS services include individual, group, and couples counseling services, health coaching, psychiatric services, and workshops and discussions. (919) 660-1000. https://studentaffairs.duke.edu/caps
  • Blue Devils Care: A convenient and cost-effective way for Duke students to receive 24/7 mental health support through TalkNow and scheduled counseling. bluedevilscare.duke.edu
  • Two-Click Support: Duke Student Government and DukeReach partnership that connects students to help in just two clicks. https://bit.ly/TwoClickSupport

Attendance Policy Related to COVID Symptoms, Exposure, or Infection.

Student health, safety, and well-being are the university’s top priorities. To help ensure your well-being and the well-being of those around you, please do not come to class if you have symptoms related to COVID-19, have had a known exposure to COVID-19, or have tested positive for COVID-19. If any of these situations apply to you, you must follow university guidance related to the ongoing COVID-19 pandemic and current health and safety protocols. If you are experiencing any COVID-19 symptoms, contact student health. 919-681-9355.

To keep the university community as safe and healthy as possible, you will be expected to follow these guidelines. Please reach out to me and your academic dean as soon as possible if you need to quarantine or isolate so that we can discuss arrangements for your continued participation in class.

Tentative Schedule

Our most up-to-date lecture and lab practical schedule is available as a google calendar at this link. Below is a tentative schedule for the semester, which is subject to change. The dates of the lab practicals have not yet been assigned.

DateTypeTopicDetailsPre-class AssignmentsPost-class Assignments
Week 1: Introduction, group norms, establishing team schedules
Jan 14LectureIntroduction to Biotech Design II• Syllabus review
• Classroom and group norms
• Special topics lectures
• Submit first round budgetary items and revised semester plan• Set up weekly meetings with TAs/Dr. Chory
• Confirm safety trainings are up to date through May 2023
Week 2: Designing, archiving, testing DNA designs
Jan 21LectureProject management tools• Gantt chart timelines
• Kanban boards
• MeisterTask/MS Teams
• Complete CITI Responsible Conduct of Research (RCR) training• Submit first round of cloning primers/gBlocks by Friday, January 26
Week 3: Project management, team organization
Jan 28LectureDNA Assembly— Reading & Writing• Benchling for plasmid design
• Primer design for cloning/qPCR
• Invite TAs/Dr. Chory to team PM tools
LabCell Culture & Transformations• Cell culture (mammalian, bacteria, yeast, etc.)
• Transformation/transfection
Week 4: Experimental design and statistics
Feb 4LectureThe “right” statistical tests• Nonparametric tests
• Using R/Seaborn for data analysis
• Rigor Rapids board game
• Submit cell lines, plasmids, etc. for purchase• Submit cell lines, plasmids, etc. for purchase using this Order Request Form: https://forms.gle/37c43kHXHg931bmN6
LabProtein & RNA Expression• Yeast/E. coli— Western blotting
• Mammalian— RNA extraction/qRT-PCR
Week 5: Team check-ins
Feb 11LectureSharkTank + BioBucks• 10-15 minute project pitch (with slides) for each team• Interview a stakeholder— one-page summary of meeting
• Submit slides from lab meeting
LabAAV & Flow Cytometry• Mammalian— AAV transduction & flow cytometry
Week 6: Ethical Considerations and Communication in Biotech Research
Feb 18LectureEthics in the research process• Identifying research dilemma in technology deployment• Peer assessment 1 due (CATME)#REF!
LabProtein Quantification• ELISA for quantitation of important protein of interest
Week 7: Presentation feedback, manuscript/poster presentations
Feb 25LectureHow to Present• How to give a poster presentation
• Requirements for manuscript/peer review process
• Make-up week for lab practicals
• None— focus on mid-term presentation and lab practical submissions
LabBinding Kinetics• SPR assay for binding affinity/kinetics
Week 8: Mid-semester presentations
Mar 4LectureMid-semester team presentations• Pitch deck + research results
• Next steps
• Submit slides and updated reports
• Submit Lab Practical reports by Friday
Lab• Make-up week for lab practicals
Week 9: Spring Break— No class
Mar 11None
Week 10: [Tentative] Intellectual property and next steps in biotechnology advances
Mar 18LectureGuest LectureTBD• Poster/report introduction draft due
Week 11: [Tentative] Advancing gene therapies in the clinic
Mar 25LectureGuest LectureTBD• Poster/report materials & methods draft due
Week 12: [Tentative] Pursuing careers in biotechnology
Apr 1LectureGuest LectureTBD• Updated pitch deck + video due
Week 13: [Tentative] The role of the government in biotechnology advances
Apr 8LectureGuest LectureTBD• Preliminary poster/report results draft due
Week 14: [Tentative] Navigating the Biotech Startup Ecosystem
Apr 15LectureGuest LectureTBD• Complete poster draft (date TBD)• Finalized posters due 24 April for printing
Week 15: Class feedback and wrap-up
Apr 22LectureFinal Lecture: Wrapping up your BME Journey• Peer assessment 2 due (CATME)