9.17 | Spring 2013 | Undergraduate

Systems Neuroscience Lab


Course Meeting Times

Lectures: 1 session / week, 1 hour / session

Recitations (Dry Lab): 1 session / week, 1 hour / session

Labs (Wet Lab): 1 session / week, 4 hours / session


Course Description

Systems Neuroscience Laboratory consists of a series of laboratories designed to give students experience with basic techniques for conducting systems neuroscience research. It includes sessions on anatomical, neurophysiological, and data acquisition and analysis techniques, and the ways these techniques are used to study nervous system function. Training is provided in the art of scientific writing with feedback designed to improve writing skills. Assignments include weekly preparation for lab sessions, two major research reports and a series of basic computer programming tutorials (MATLAB®). The class involves the use of experimental animals. Enrollment is limited.

Primary Course Goals

  • Gain familiarity with an overview of basic techniques in systems neuroscience
  • Gain hands-on experience with these techniques
  • Gain competence and understanding of the primary method of writing scientific communication—the research paper

Expected Out-of-Class Work

  • Review of lecture notes and readings for upcoming lab session and recitation
  • Quiz preparation
  • Preparation of lab notebook each week
  • Reading and understanding of each recitation paper (one per week)
  • Preparation of (2) research reports in the form of short scientific papers
  • Completion of MATLAB® tutorials
  • Supplemental readings related to the lab session (optional)


In-lab quizzes (no make-ups allowed) 30%
MATLAB® tutorials 10%
2 research reports (~10 pages double spaced) 40%
Laboratory notebook 10%
Participation: In-lab performance 6%
Participation: Recitation performance 4%


A quiz will be given at the start of most labs (see the calendar for details). We generally allow 20 minutes to complete the quiz. The time allotted to complete the quiz begins at the start of class, not when you walk in the door. If you arrive to the lab after the allotted quiz time, you will get a 0 for the quiz (because quizzes are discussed right after they are given).

Quiz questions come from lecture material and assigned readings for the session, including recitation papers. The quiz will cover basic concepts and important details related to the lab.

Quizzes are not returned to students. Quiz answers are generally discussed immediately after the quiz. Thus, you immediately know your quiz performance. If you would like to discuss a quiz further outside of class, please contact the teaching staff that gave the quiz.

Research Reports

You will learn how to write a short scientific paper. Because you will typically work in teams of 2–3 in each lab, the data in each research report will often be identical. However, we expect each of you to write your own research report. Duplicate sentences or paragraphs in research reports are considered to be a form a plagiarism and, as MIT students, you already know that this is extremely unethical. If this, or any other form of plagiarism (e.g. sentences copied from references without citation) is apparent in your research report, the report will receive a grade of zero, and you may be referred to the MIT Committee on Discipline. Further information about plagiarism and its consequences can be found on MIT’s academic integrity website.

Final Letter Grade

See the grade worksheet (PDF) for details on how the final grade is calculated.

The grade cut-offs for this course are:

  • 900 points or above = A
  • 800–899 points = B
  • 700–799 points = C
  • 600–699 points = D

We will do our very best to hold to these cut-offs, but please note that the final exact cutoffs are at the instructor’s discretion. Historically, most students that attend the lectures and recitations, prepare for each lab, show up on time to take the quiz, put sincere effort into the labs, and turn in all assignments on time get A’s and B’s in this course.

We will approach students that are in danger of receiving a D or below prior to Drop Date. If you cannot live without knowing exactly where you sit at any given moment in the course on the A/B/C/D lines, you are responsible for computing your own estimate based on your grades to date, the grade sheet at the end of this document and the cut-offs above. If you need to obtain any of your quiz grades, please see the lab supervisor.

If you have any questions regarding these policies, please feel free to contact us at any time. If you are unwilling to accept all of these grading policies, please drop the class now. If you continue in the class, you indicate acceptance of the grading policies.

Grading Policy

Quizzes are reviewed just after they are taken, but are not returned to you. If you would like to see your quiz or discuss any of your grades, please contact the lab supervisor. You are also welcome to contact the appropriate instructor. Details on how research reports and lab notebook are graded are described in the assignment section. The “in-lab performance” grade is based on your attendance in lab, the teaching staff’s impression of how well prepared you are for the lab, and, thus, how you perform in the lab. The “recitation performance” grade is based on your attendance in recitation and the teaching staff’s impression of how well prepared you are to discuss the papers presented.


This is historically a popular course, and we have opened it up to the maximum number of students that we can teach and still provide a hands-on experience. First priority is given to course 9 students. Additionally, seniors are given priority over juniors, who have priority over sophomores. Attendance on the first day of class is required to secure a position in the course. If you have questions about getting into the course, those questions should be directed to the undergraduate administrator in the BCS headquarters.

Adding 9.17:
Students on the course wait list that attend the first week will have priority if a spot becomes available by the start of week 2. No adds will be allowed after the end of week 2.

Dropping 9.17:
We understand that you may decide to drop the course for any reason. However, because space is limited we kindly ask that you let Susan Lanza in the BCS office know of your drop by the start of week 2. If you do not do this or decide to drop the course at a later date, you may get on the wait list for the course in a future year, but first-time entrants on the wait list will get priority.

Listener status for 9.17:
Listener status is currently not allowed in 9.17.

Class Structure

Introductory Lecture

What are the principles for this week? How do they fit in the big picture? How will the lab run?

Recitation Section

Discuss papers that focus on the applications of lab techniques in real science experiments.

Lab Section

Quiz on the upcoming lab (~20 minutes) and review of the quiz.
Hands-on lab session (3–4 hours)

Missed Sessions, Make-up Policies, and Late Policies

We would really like this to be a fun learning experience for you. In an ideal world, all students would be able to make all the sessions and learn from their experience. The biggest loss to you is the lost opportunity to learn and experience something new—something that only you can value for yourself. However, in fairness to all of the students, we have established the following policies so that you will understand how missed sessions will affect your grade.


There is no explicit penalty for missing a lecture, but it will make it much more difficult to grasp the material and to do well on the quizzes and the lab.


In addition to contributing to your participation grade, the recitation sessions will include paper presentations that will help you to understand class material and will show you some applications of lab techniques in the real world. Some of the material covered in these papers will appear on quizzes. Also these sessions are opportunities for you to ask questions about class material and lab reports. Because your recitation participation grade is dependent on attendance, it is in your best interest to attend your recitation.

Lab Sessions

While we understand that students will not always be able to attend every lab session, we ask you to please realize that there is a great deal involved in preparing and cleaning up after each session. Given this, and the fact that the point of a lab course is for you to spend time in the lab (not simply to display knowledge), your attendance in these sessions is an important part of your grade. The quiz at the beginning of each lab session serves not only for you to show us that you have prepared for the lab, but to indicate your full attendance in the lab. Thus, in fairness to all students, no quiz make-up is allowed. Depending on the session and the willingness of your lab partners to share results with you, your research report grade may also suffer indirectly. Note, however, that we will count the best 10 out of 11 quizzes and lab notebook grades. This means that you can miss one lab/quiz session with only minor impact on your final grade.

No lab make-up sessions are possible. Each lab session takes a tremendous amount of time to set up and to clean up, and we have only one lab section per week. Therefore, if you miss a lab session, you will have no opportunity to make up that session.

Late Research Reports

The research reports due dates are indicated in the syllabus. All research reports are due by 5 pm on the indicated due date.

To ensure that your research report is verified as being turned in on time, your research report should be turned in to the lab supervisor. It is your responsibility to give the lab supervisor a hard copy (no online copies will be accepted) before the 5pm deadline. Research reports turned in after this moment in time will not be graded and will receive zero points.

We understand that unforeseen circumstances may prohibit you from turning you research report in on time. MIT has well-established mechanisms to facilitate the communication of such circumstances. In particular, the instructors can use official letters from Student Support Services on your behalf to grant case-by-case, temporally-limited extensions of due dates. In addition, each student is given one “free” no-penalty extension of the research report. If a student uses the free extension option, you will have an additional two days from the original due date and time to submit your report. Please indicate that you are using your free extension by writing “free extension” on the front of your research report. The lab supervisor will give submission instructions to students using the extension option as needed. Make sure to inform the lab supervisor via email that you are taking your extension before the paper is due.

Teaching Assistants, Recitation Instructor, and Lab Supervisor

There are three TAs for the entire course plus a lab supervisor. At least one TA and the lab supervisor will be present at each lab session. If you have questions for the TAs regarding the lab, quiz, research report, etc., please contact the TA(s) that were assisting in the lab.

All research reports and projects should be turned into the lab supervisor, unless otherwise stated. We will provide more information about submissions later in this handbook. Please see the class site for TA and lab supervisor contact information and please feel free to ask them (and the instructors) for help.

“MATLAB and Simulink are registered trademarks of The MathWorks, Inc. See www.mathworks.com/trademarks for a list of additional trademarks. Other product or brand names may be trademarks or registered trademarks of their respective holders.”

Animal Use Notice

It is not possible to study the nervous system without handling actual neural tissue. Thus, several of the classes will use animals (rats, frogs, cockroaches, flies). We have made every attempt to reduce the number of animals used in this course. Several labs use simulations instead of animals.

All animal procedures are in accordance with NIH guidelines are approved by MIT’s Committee on Animal Care. We will have a presentation on the use on animals in research and teaching from an MIT veterinarian. If you are uncomfortable with the use of animals, please contact one of us immediately after the first class.

Course Info

As Taught In
Spring 2013
Learning Resource Types
Lecture Notes
Written Assignments