20.309:Course Information

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(Overview of laboratory modules)
(Overview of laboratory modules)
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[[Image:DNA Melting Apparatus Picture|right|150px|DNA Melting Apparatus]]'''''Resistive networks, filters, and op-amp circuits for measurement'''''
[[Image:DNA Melting Apparatus Picture|right|150px|DNA Melting Apparatus]]
'''''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.
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.
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[[Image:20.309 Fluorescence Microscope Picture|right|150px|Fluorescence Microscope]]
'''''Fluorescent microscopy, image processing, and optical traps'''''
'''''Fluorescent microscopy, image processing, and optical traps'''''

Revision as of 11:49, 6 September 2007

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
Monday10:00 AM - 6:00 PM
Tuesday1:00 AM - 9:00 PM
Wednesday1:00 AM - 9:00 PM
Thursday10:00 AM - 6:00 PM
Friday10:00 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


DNA Melting Apparatus

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 facilities

Lab stations

There are 8 lab stations in room 16-352. Each station is equipped with:

  1. anti-vibration optical table
  2. analog oscilloscope
  3. triple output power supply
  4. function generator
  5. instrumentation amplifier
  6. toolbox
  7. computer workstation with data acquisition card

Station number 3 is reserved for instructor use at all times.


Lab stations are equipped with PCs running Windows XP. Each PC has a data acquisition card that is connected by a long cable to a signal breakout box at the lab station. MatLab and LabVIEW software are installed on all lab PCs.

Lab PCs are members of the WIN.MIT.EDU domain. Press ctrl-alt-delete to log on. Make sure the Log On To: dropdown menu is set to ATHENA.MIT.EDU (Kerberos Realm). Use your Athena username and password.

The first time you log on, a Windows profile for storing all of your files and settings will be created in your home directory. From then on, your My Documents and Desktop folders will be available on whichever machine you log on to.

Store files in your My Documents folder. Do not keep large files on your desktop. (Use a shortcut to large items instead.) This will dramatically decrease the amount of time it takes to log in. (If you are curious why this is so, see: http://web.mit.edu/win/user_profiles.html.)

Your Windows home directory will be mounted on H:. In addition, your Athena home directory will be mounted on U: and /mit/afs will be mounted on Z:.

IS&T maintains a help page for the WIN domain at http://web.mit.edu/win/help.html.

Course locker

The 20.309 course locker and wiki contain virtually every computer file you will need for the course. To access the locker on an Athena workstation, type attach 20.309 and then cd /mit/20.309. Use the Sesktop or Start Menu shortcut to access the locker from any PC in the lab.

Course grade

  • 50%: Written reports for lab modules

You will work in pairs throughout the semester, but you will submit individual lab reports. Please see the section on lab reports below.

  • 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 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 tables appropriately. If a table 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. The second sentence, 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 fewer than tweny percent 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.

Lab report grading

Lab reports will be graded on a 25 point scale. An outstanding report:

  • Demonstrates mastery of the theory and practical implementation of the key techniques used in the experiment.
  • Presents results for each of the required experimental procedures
  • Draws appropriate conclusions from the data
  • Contains a thorough, correct, and well explained analysis
  • Address shortcomings of the experimental procedure and problems that cropped up during experimentation
  • Acknowledges everything that is not original work with an appropriate citation
  • Is well communicated

Outstanding reports will receive a numerical grade of 23-25 points.

Reports with minor deficits in one or two areas will receive an excellent score in the range of 20-22 points.

Reports with important shortcomings in one area will be awarded 17-19 points.

Manuscripts not meeting the above criteria will be graded accordingly.

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