585.685.81 - Methods in Neurobiology

Applied Biomedical Engineering
Fall 2023


Neurobiology is the study of cells of the nervous system and the organization of these cells into functional circuits that process information and mediate behavior. In this course we will explore molecular and cellular aspects of neuronal physiology, their organization into higher systems and approach methodologies used to analyze CNS function at different levels. Such techniques will include recent progress in whole brain imaging, advances in fluorescence microscopy and optogenetics, the basics of single-cell sequencing and the use of cellular, organoids or animal models in neuroscience. We will also discuss deviations from neuronal physiology such as during aging or after onset of CNS related pathologies, including neurodegenerative diseases and approaches to cell reprogramming and regeneration in order to recover cellular function.At the end of this course, students will have a broader understanding on techniques used to study neuronal function at a molecular, cellular and systemic level and will have the basics insights to infer which tools are more appropriate depending on the application.

Expanded Course Description

Prerequisites for this course include: 410.602 or 585.601 Molecular Biology; 585.601 and 602 Physiology for Applied Biomedical Engineering I and II, respectively.


Profile photo of Emanuela Colla.

Emanuela Colla


Course Structure

The course materials are divided into 14 modules which can be accessed by clicking Course Modules on the left menu. A module will have several sections including the module-at-a-glance, readings, video lectures and related content, discussions, and quizzes. Most modules run for a period of seven (7) days, from Tuesday to Monday, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

Course Goals

The goals of this course are to develop critical and creative thinking through proposing and planning new ideas to be applied to the field of Neurobiology. Students will learn state of the art techniques, research strategies and important concepts relevant to neuroscience research and build from that to design new strategies or applications to answer biological questions. Each week, students will elaborate short research plans to test ideas in neurobiology. By the end of this class, students will have accumulated an extensive amount of exposure to research writing and experimental planning.

Course Learning Outcomes (CLOs)


No textbook purchases required. The course has many assigned readings that are available through EReserves and linked through the Canvas course site.

Readings provided in each module are mainly scientific reviews, research articles or technical papers and therefore describe topics and experiments in very detailed manner. Students are NOT required to learn all the details but to grasp general ideas about a specific subject as presented in the video or Powerpoint presentations.

Student Coursework Requirements

It is expected that each module will take approximately 10-14 hours per week to complete. Here is an approximate breakdown: reading the assigned articles (approximately 4-6 hours per week), listening to the audio annotated slide presentations (approximately 1.5-2 hours per week), completing discussions and case studies (approximately 5-6 hours per week). 

This course will consist of following basic student requirements:

  1. Discussion board assignments (20% of final grade)

This course has 12 graded discussions. Eight of them follow a specific format described more fully in module 1. These eight discussions will require students, on a rotating basis, to identify and post interesting media related to the materials presented that week for the rest of the class to discuss. All 12 graded discussions are worth 12 points each, weighted equally.

The topic of discussion must be posted by the evening of day 2 (Thursday) whereas first responses must be posted by the evening of day 4 (Saturday). Posting a response to the discussion question is part one of your grade for module discussions. Part two of your grade for module discussion is your interaction (i.e., responding to classmate postings with thoughtful responses) with at least one classmate. 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.

  1. Case Studies (40% of final grade)

There are five case studies in the course. The case studies run over 2-week periods. During the first week, each student prepares and uploads an individual case study. During the second week, each student is paired with another student to review and discuss each other’s work. More information about the case studies is available in the modules where they are presented.

  1. Unit Assessments and Final Exam (40% of final grade)

There are 3 unit assessments, in modules 6, 10, and 13. The final exam is in week 14.  All are weighted equally.


Grading Policy

Assignments are due according to the dates posted in the Canvas course site. Students may check these due dates in the Course Calendar or the Assignments in the corresponding modules. There is no late policy for individual assignments but after one month from the due date discussion threads will be closed and students will not be able to post. Constant inability to turn in assignments on time will affect the final grade.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week. A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

The following grades are used for this course: A+, A, A– (excellent), B+, B, B– (good), C (unsatisfactory), F (failure), I (incomplete). A grade of F indicates the student’s failure to complete or comprehend the course work. 

A course for which an unsatisfactory grade (C or F) has been received may be retaken. The original grade is replaced with an R. If the failed course includes laboratory, both the lecture and laboratory work must be retaken unless the instructor indicates otherwise. A grade of W is issued to those who have dropped the course after the refund period but before the drop deadline. The transcript is part of the student’s permanent record at the university. No grade may be changed except to correct an error, to replace an incomplete with a grade, or to replace a grade with an R. 

The Whiting School assumes that students possess acceptable written command of the English language. It is proper for faculty to consider writing quality when assigning grades.

For incomplete grades, please see the Graduate Programs catalogue for the Whiting School of Engineering.

The course grading scale is the following:

Score RangeLetter Grade
100-98= A+
97.9-94= A
93.9-90= A−
89.9-87= B+
86.9-83= B
82.9-80= B−
79.9-70= C
<70= F

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 values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

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.