20.309:Course Information

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20.309: Biological Instrumentation and Measurement


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Course Meetings

Lecture: T/R 12:00n-1:00pm (56-180)

Recitation: F 12:00n-1:00pm (56-162)

Lab: open scheduling, approximately 6 hours per week (16-352)

Lab Hours and Scheduling

The lab will be open approximately 40 hour per week. Students are responsible for scheduling sufficient time in the lab to complete assignments before the deadline. Generally, the opening hours will be:

Lab Opening Hours
Monday 10:00 AM - 6:00 PM
Tuesday 1:00 AM - 9:00 PM
Wednesday 1:00 AM - 9:00 PM
Thursday 10:00 AM - 6:00 PM
Friday 10:00 AM - 6:00 PM

You must sign up at least 24 hours before coming to the lab. Use the LAB SIGNUP link above in the title bar.

The lab is located in room 16-352.

Lab attendance is mandatory. There will be no make-up labs, except extraordinary circumstances.

Lab phone: 617-324-1634


The chief hazards present in the 20.309 Lab come from laser radiation, chemical and biological materials, and electric equipment. Some simple precautions will make your time in the lab much safer.

Get to know the 20.309 Safety Page. Read the safety precautions in each lab manual.

Overview of Laboratory Modules


Resistive networks, filters, and op-amp circuits for measurement

The first part of the course focuses on electronics. Over a series of labs, we will build several types of commonly used electronic circuits and combine them implement a system for measuring DNA melting curves. This section will also provide an introduction to computer control and data acquisition, including LabVIEW and MATLAB software.


Scanning probe microscopy

We will learn to configure and use "home-built" atomic force microscopes (AFMs) for imaging surfaces with nanometer-scale resolution, conducting sensitive force measurements, and exploring the ultimate detection limits of microcantilevers. Such instruments are essential for investigating the mechanics of single biomolecules, cellular adhesion and modulus, as well as the physical properties of biomaterials. The goal of these labs is to gain hands-on experience with these instruments in the lab and understand the basic principles that they use to achieve exquisite sensitivity.


Fluorescent microscopy, image processing, and optical traps

Approximately half of the semester is devoted to optical microscopy and imaging. The lectures will cover geometric optics, Fourier optics, and optical instrumentation design, the fundamentals of image processing and 3D microscopy. In the labs, we will build microscopes for white light and fluorescent imaging and apply them to studying cellular mechano-transduction based on particle tracking and immunolabeling. We will also use optical traps for high sensitivity measurements of bacterial flagella torque generation, and get some hands-on experience with two-photon and confocal microscopes.

Lab report guidelines

The purpose of your report is to convey as clearly as possible which physical phenomena you examined in the lab, the means you employed, and what you learned. The report should stand on its own; it should not read like a problem set. There is no need for the report to be lengthy. Focus on the essentials.

Imagine that you are writing the report for a classmate who has not yet done the lab. The intended audience for your report has a deep understanding of the subject. As such, lengthy derivations and explanations are not necessary. The reader would very much like to understand what you did in the lab, what sort of problems you ran into, how you analyzed your data, and what you concluded.

Your report does not have to be written like a formal scientific paper. Feel free to use whatever organization works for you so long as it includes all of the information. Follow the content and style guidelines below.

Introduce the subject

Begin with a paragraph or two explaining why you went to the lab. What were the key questions you set out to answer? What techniques did you apply to the problem?

Explain the apparatus and procedure

Some lab exercises involve significant design and construction work. Others utilize complex systems that were built by others. In either case, the apparatus you used in the lab must be documented in your report. Block diagrams, schematics, photographs, and text descriptions are all excellent ways to describe an apparatus.

Design documentation should be sufficiently detailed to enable another person to build a similar piece of equipment. Include component values and reference designators (Rl, Cf, L1, etc…) on schematics. Explain in the text why you chose the values you did. If you chose to implement a portion of your apparatus differently than the lab manual suggested, explain why. If you wrote a program, explain what it did in the body of your report and include the source code in an appendix.

Detailed documentation is available for the predesigned pieces of equipment in the lab (such as the AFM and the optical trap). In these cases, focus on the aspects of the machine that are essential to understanding your data analysis. A simple block diagram and a few paragraphs will meet the requirements.

Once you have documented the apparatus, explain how you used it and what measurements you took.

Explain your analysis

Tell what steps you took to analyze your data. As in the other parts of your report, focus on what is important. It is not necessary to reproduce each step of every calculation. Make sure the reader understands what you did, though.

Say what would you do differently next time

The instruments and procedures you will use in the lab are not perfect. Explain what factors limited your measurements how you could improve the results.

Answer questions posed in the lab manual

Ensure that your report addresses all the questions posed in the lab manual. If there is not a natural place to do this in the body your report, put the answers in a section of their own.

Present data properly

  • Figures must be numbered, descriptively captioned, and discussed in the text.
  • Plot axes must be labeled with a brief, informative title including units.
  • Pictures must have a scale. (Pictures of your apparatus are an exception.)
  • Chartjunk is forbidden.
  • Use charts appropriately. If a chart can be replaced by one or two sentences, do so.
  • Try not to use screen captures.

Do not present every piece of raw data you gathered. Put in only things that are important, in a clear and concise format. If for some reason you have a large body of extremely interesting data to present, put it in an appendix and refer to it in your report. If you have a large body of uninteresting data, leave it out.

Write tight prose

  • Avoid the first person.
  • Use active verbs.
  • Eliminate unnecessary words.

It is common practice in scientific writing to avoid using the pronouns I and we. This is changing slowly; however, it is an excellent habit to minimize the first person in your scientific writing. The author of a first person sentence in a scientific paper has frequently misidentified the true subject of a sentence. Consider the following 4 versions of a sentence:

  1. I ran the experiment three times and calculated an average power of 1.21 GW.
  2. The experiment was run three times and an average power of 1.21 GW was calculated.
  3. Three experimental runs yielded a calculated average power of 1.21 GW.
  4. Three experimental runs yielded an average power of 1.21 GW.

In this example, substituting the subject “The experiment” for “I” eliminated the first person pronoun in sentence number 1, resulting in somewhat preferable sentence 2. Sentence 2, though, is undesirable because it contains the passive verb forms "was run" and "was calculated." Passive voice is common in scientific writing; however, that does not mean you are required repeat the offense.

It is impossible to completely eliminate passive sentences from scientific writing. But that doesn’t mean you can’t try. See if you can limit your use of the passive voice to tweny percent or less of the verbs in your report.

Sentence 3 is preferable to number 2 because it uses an active verb. But it still could be tighter. Average values are necesarily calculated. Unless required to differentiate between several possible averages, remove the redundant verbiage.

Write your own report

In 20.309, you will work collaboratively in the lab. The report you submit must be entirely your own work. Any words, data, images, code, or other intellectual property you take from somebody else must be appropriately cited. Plagiarism is unacceptable.


  • 50%: Written reports for lab modules

You will be working in pairs throughout the semester, but you will be submitting individual lab reports.

  • 15%: Oral presentation

You will each give a 12 minute presentation on a selected lab module or a relevant journal paper.

  • 15%: Homework assignments

These will include questions related to lecture material, lab modules, and selected journal articles.

  • 10%: Lab quizzes

These are intended to help you prepare for the experiment you are performing. The questions will be straightforward and should take about 5 minutes before you begin working on each lab.

  • 10% Participation during lectures and laboratory modules

Your participation is essential to learning during the semester. This includes attendance at lectures and your peers' presentations.

Lab Report Grading

  1. Presentation of Data (10 pts.)
    • all figures have clear purpose, have a figure number and caption, and are discussed in text
    • data plots:
      • appropriately chosen/organized (e.g. curves overlaid or compared, when appropriate, correct scales, etc.)
      • axes labeled with quantities/units
      • quality of data
    • no "data dumping" or screen captures (unless explicitly specified)
  2. Analysis/discussion (10 pts.)
    • demonstrates understanding of key concepts/methods
    • coherent, logical reasoning, clear thought process
    • show key numeric parameters; include important calculations and results
    • appropriate data processing applied, described and justified
    • draw conclusions supported by the data
  3. Overall quality (5 pts.)
    • report typed, well-organized, length appropriate say what you need to – not more or less
    • report requirements met
    • sufficient time spent in the lab
    • citation of any material that isn't your own (e.g. things you looked up on the web, in literature; data from others in the class; be sure to list with whom you worked on the lab)