585.751.81 - Immunoengineering

Course Structure

The course materials are divided into modules which can be accessed by clicking Modules on the course menu. A module will have several sections including the overview, content, readings, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

Immunoengineering is a quickly growing field where engineering principles are used to better understand the dynamics of the immune system and enhance the efficacy of current immunotherapeutics. This course will provide relevant background in our understanding of various immune responses including to pathogens, self, allergens, cancer, and biomaterials. An in-depth engineering perspective and approach will be taken in the analysis of these responses and the development of novel therapeutics. Topics include systems immunology, genetic engineering, nanotechnology, hydrogels, biomaterials, vaccines, cancer immunotherapy, autoimmunity, tissue engineering, stem cells, viruses, bacteria, etc.

Module Outline

1    Immunoengineering: A New Frontier

2    Immune Response: Pathogens

3    Immune Response: Autoimmunity, Allergen

4    Immune Response: Cancer

5    Immune Response: Biomaterials

6    Midterm Exam and Immune System Review      

7    Engineering Therapies: Pathogens

8    Engineering Therapies: Autoimmunity, Allergens

9    Engineering Therapies: Cancer

10   Engineering Therapies: Biomaterials and Implants

11   Engineering Therapies: Biomaterials and Tissue Engineering

12   Engineering Tools: Immunoprofiling

13   Engineering Tools: Modeling

14   Final Projects/Presentations

Course Goals

By the end of this course, you will be able to:

1. Explain various types of immune responses to someone not within the field of immunoengineering (i.e. pathogens, self, allergens, cancer, biomaterials)
2. Identify the advantages and disadvantages of current immunotherapies
3. Examine the applications of engineering principles that have led to advancements in the field of immunology
4. Apply principles of engineering to advanced topics in immunoengineering within problem sets and quizzes
5. Evaluate current advances in the immunoengineering field
6. Propose how engineering can further contribute to the field of immunology

Textbooks

No textbooks are needed. All readings are provided or available online. However, some students have mentioned that having a basic physical immunology textbook has been beneficial. You can get old editions of the following textbooks that would be affordable online, but are not required:

• Janeway's Immunobiology by Kenneth M. Murphy
• How the Immune System Works (The How it Works Series) by Lauren M. Sompayrac

Student Coursework Requirements

1. Participation (Online Quizzes and Module Discussions) (15% of Final Grade Calculation)

Module 1-5 will have a short online quiz that you must complete as part of your participation grade. The quizzes are designed to permit you to self-assess your knowledge on the topics that are covered and will help you prepare for the exam. You are responsible for carefully reading all assigned material and being prepared for discussion. You must complete the online reading, view the videos, and answer the questions in the online quiz and receive a score of at least 90% on the module quizzes prior to receiving access to the module assignment.

Post your initial response to the discussion questions by 11:59 PM on day 4 (Saturday) for that module week. Posting a response to the discussion question is part one of your grade for module discussions (i.e., Timeliness). You are encouraged to use recent references from literature searches in your discussion postings.

Part two of your grade for module discussion is your interaction (i.e., responding to classmate postings with thoughtful responses) to at least one classmate (i.e., Critical Thinking) by 11:59 PM on day 7 (Tuesday). Just posting your response to a discussion question is not sufficient; we want you to interact with your classmates. Be detailed in your postings and in your responses to your classmates' postings. Feel free to agree or disagree with your classmates. Please ensure that your postings are civil and constructive. You are encouraged to use references in responses to your classmates’ postings.

We will monitor module discussions and will respond to some of the discussions as discussions are posted. In some instances, we will summarize the overall discussions and post the summary for the module.

Evaluation of preparation and participation is based on contribution to discussions.

2. Assignments (20% of Final Grade Calculation)

Assignments will include a mix of qualitative assignments (e.g. literature reviews, model summaries), quantitative problem sets, and case study updates. Make sure your name, the assignment number, and a page number indicator (i.e., page x of y) are in the header of each page of your submissions. Each problem should have the problem statement, assumptions, computations, and conclusions/discussion delineated. All Figures and Tables should be captioned and labeled appropriately.

All assignments are due according to the dates in the Calendar (generally by 11:59 PM on day 7 (Tuesday)) and must be submitted as pdf or Word files.

Late submissions will be reduced by one letter grade for each week late (no exceptions without prior coordination with the instructors). In other words, the maximum grade for an assignment up to one week late is B, up to two weeks late is a C, and up to three weeks late is a D. Assignments will not be accepted after 4 weeks and will be given a grade of “0”. We will drop one homework assignment grade to accommodate for unforeseen situations.

 One of the main methods of learning and demonstrating mastery of course concepts will be incorporated in your final project. You will produce 2 final products for this course’s final project surrounding the same topic. You will come up with an engineering solution to a current disease or challenge in immunology. This will be in the form of a short, written proposal (similar to an R21) and a short pitch presentation (between 3 and 7 minutes) using a narrated PowerPoint presentation (or equivalent presentation software of your choice) using Voicethread. We will post specific details and instructions for each deliverable and what you will be evaluated on. Here is a brief outline of the project timeline and assignments:

Project Outline and Module Milestone Assignments

Grading Policy

Qualitative assignments are graded as follows:

100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis].

89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place].

79–70 = C—Majority of parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [generally competent; information is thin and commonplace].

<70 = F—Some parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rudimentary and superficial; no analysis or insight displayed].

Quantitative assignments are graded as follows:

100–90 = A—All parts of question are addressed; All assumptions are clearly stated; All intermediate derivations and calculations are provided; Answer is technically correct and is clearly indicated; Answer precision and units are appropriate.

89–80 = B—All parts of question are addressed; All assumptions are clearly stated; Some intermediate derivations and calculations are provided; Answer is technically correct and is indicated; Answer precision and units are appropriate.

79–70 = C—Most parts of question are addressed; Assumptions are partially stated; Few intermediate derivations and calculations are provided; Answer is not technically correct but is indicated; Answer precision and units are indicated but inappropriate.

<70 = F—Some parts of the question are addressed; Assumptions are not stated; Intermediate derivations and calculations are not provided; The answer is incorrect or missing; The answer precision and units are inappropriate or missing.

The research paper will be graded as follows:

100-90 = A - Superior submission in all aspects. High quality research and analysis of the subject with excellent support, discussion, and justification at a level appropriate for a competent engineer with excellent organization and presentation. 

89-80 = B - good submission in all aspects. Acceptable research analysis of the subject with adequate discussion and justification of major points.  Good organization of paper that is generally easy to follow and proceeds logically through the material. Presentation of paper is acceptable, may be missing minor elements like section headings or have minor spelling/grammar errors.  An acceptable number of references are provided.

79-70 = C - paper has major flaws and is not representative of a quality graduate level submission.  Major gaps in research, analysis and coverage of the subject; may have minor technical inaccuracies. Organization is lacking, with major breaks in logic and flow.  Presentation is below average, with missing elements and spelling/grammar errors that make paper difficult to read.  The number of citations is inacceptable or incomplete.

<70 = F - paper has major inaccuracies and incomplete analysis, plagiarized portions, and/or entire missing sections.  Presentation or organization errors are so egregious that paper is judged to be entirely unacceptable for submission.

The pitch presentation will be evaluated by the following elements:

1. Format and Content (50%)
2. Delivery (50%)

The presentation will be posted on Blackboard using VoiceThread and will be graded as follows: 100-90 = A - Complete and organized content; Innovative presentation structure; Superior presentation includes succinct overview of all the required elements; excellent use of multimedia content (e.g. video); and within the time limit

89-80 = B - Complete and organized content; Easy to follow presentation structure; Engaging presentation includes succinct overview of all the required elements; good use of multimedia content (e.g. video); and within the time limit

79-70 = C - Complete and organized content; Basic presentation includes succinct overview of most of the required elements and is reasonably within the time limit

<70 = F - Incomplete content; little or no organization; Presentation does not cover all the project elements, and is over or under the time limit

Final grades will be determined by the following weighting:

Course Policies

Late submissions:

Late submissions will be reduced by one letter grade for each week late (no exceptions without prior coordination with the instructors). In other words, the maximum grade for an assignment up to one week late is B, up to two weeks late is a C, and up to three weeks late is a D. Assignments will not be accepted after 4 weeks and will be given a grade of “0”. We will drop one homework assignment grade to accommodate for unforeseen situations.

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students. This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University is committed to providing welcoming, equitable, and accessible educational experiences for all students. If disability accommodations are needed for this course, students should request accommodations through Student Disability Services (SDS) as early as possible to provide time for effective communication and arrangements.  For further information about this process, please refer to the SDS Website.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically.  For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity.    If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.