Sophisticated measurement techniques play a central role in modern biological research. 20.345 is a hands-on course that allows students to explore some of the most advanced methods in use. The course emphasizes application of optical, electronic, micromechanical, and microfluidic technologies to biological measurement problems on a scale from single molecules to whole organisms. There will be one short lab exercise over the first three weeks of the semester. You will develop a written proposal for a substantial, original project that you will execute over the last eleven weeks. Your project will be an opportunity to pursue a specific technique in depth. You will have many chances to work on your writing, presentation, and project planning skills. Active participation is a vital part of the course.
Students should have a background in physics, biology, computer programming, and linear systems. Tutorials will be given during the first weeks of class for students who have not previously studied geometric optics or those in need of a refresher. Review sessions on electronics and linear systems will also be offered.
Lectures will be on Tuesdays and Thursdays at 12:00 PM in room 16-336. The first few lectures will introduce the structured lab exercise and discuss projects. The third lecture will include a mandatory discussion of laser safety. Other lectures will cover multidimensional transforms, advanced microscopy methods, atomic force microscopy, mass spectrometry, and other techniques.
Assignments and grading
There will be one structured lab to kick off the semester, five problem sets, one exam and the primary class project. Grades will be weighted as follows:
- 20% 2 problem sets
- 50% Final project
- 10%: Class and lab participation
- 20%: Exam
A good final project must be feasible, relevant and novel. Unfortunately, the demands of novelty are frequently at odds with achievability. For the purposes of this course, feasibility is nearly always the more important consideration. Resist the temptation to choose a topic that might be more appropriate for your Ph.D. thesis. Replicating a previously reported method inexpensively, in a teaching lab environment is both noble and novel. Developing an entirely new in vitro neuronal guidance technology is folly. Work closely with your mentor to find the right balance. The lab has a modest budget for purchasing new components and equipment, if the case for them is compelling.
Students will work in groups of 3-5.
The milestones for the final project are:
- Statement of interest
- Initial proposal
- Final proposal
- 3 group progress reports
- Final presentation
- Final documentation
Statement of interest
Turn in a short statement of interest at the end of the first week of class. The statement should summarize your relevant background, identify techniques you are interested in investigating, and outline your goals this semester. Be as specific as possible. If you would like to work with microcontrollers or super-resolution microscopy, say so. Your statement will help the instructors allocate resources for the semester and identify students that are interested in similar areas.
Before you begin working in the lab, you must develop a project proposal. The proposal should clearly describe your intended goal, the reasons your work is important and relevant, the methods you intend to use, the resources that will be required, related work that others have done, and the steps you plan to take along the way. One of the project ideas presented in class may inspire you, or you may decide to develop one of your own ideas. Based on the subject area of your endeavor, you will be paired with a member of the instructional staff to serve as a mentor. Develop your proposal in close consultation with your mentor.
The value of a careful literature review cannot be understated. This frequently neglected step can make the difference between breakthrough research and a fool’s errand. A conscientious search has many benefits, not the least of which is avoiding time consuming pitfalls that have been identified by others. Turn in your literature search with your Initial Project Proposal.
Your Final Written Proposal is due at the end of the fourth week of class. Follow the project proposal outline. The proposal should be less than ten pages, excluding supplementary materials. Have your mentor review the proposal — perhaps more than once — before submitting it.
Every two weeks, you will give an update on your progress to an instructor.
Your individual progress report should:
- Detail individual achievements since the last report
- Explain how your efforts contributed to project goals
- Specify milestones to be achieved before the next report
- Explain foreseeable technical, resource, or organizational risks
- Summarize progress overall
- Demonstrate understanding of technical and organizational details of your project
In the alternate weeks, you will present your progress as a group. You should describe what you did, why you did it, what you saw, and what you did next.
Maintaining a laboratory notebook is one of the most important skills you will develop in 20.345. A good notebook is essential when you begin to develop papers or oral presentations summarizing your experimental efforts. A clear, well-written narrative that includes experimental schematics, plots of raw data, and details of your analysis will enable you to receive quick feedback and assistance from peers and lab staff. A poorly maintained notebook will prove immensely frustrating to you and your instructor. It is very diffcult to answer questions like, “Why didn't the experiment work?” or, “Why was my result off by an order of magnitude?” without being able to clearly and easily trace your efffforts using the notebook. Don't count on being able to recall any apparatus setting even one day after a lab session!
Ye olde fashioned paper lab notebooks are dependable; however, more technologically advanced solutions are encouraged. Consider keeping your notebook on the course wiki. Whatever technology you choose, entries must be contemporaneous and clear. Timestamps are automatic if you use the wiki. If you use another technology, annotate each entry with the date and time it was made. Group members should maintain a single notebook for a project.
Instructors may review your notebook at any time, including during individual progress reports and group project reviews.
Follow these guidelines:
- Organize your notebook with a descriptive table of contents. Use sections and subsections on the wiki. Don't use generic headings like “Day 1” or “Analysis”. Instead, produce records of significant milestones: e.g. "Plot of monochromator linearity over the visible spectrum", or "Monte Carlo simulation of mean slant path distance in muon TOF experiment".
- If you use a paper notebook, don't ever erase, use white-out, or tear out pages. Indicate "mistakes" by drawing a single, neat line through the item. Things may prove to be not so incorrect as initially thought. Documented errors are useful as a guide to how the experiment was done and provide clues on how to better execute the experiment next time. If you use the wiki, a complete history of entries will automatically saved.
- List your experimental objectives and how they relate to the goals of your project.
- After listing the objectives, identify the procedures you will have to perform, the data you must obtain, and the required calibrations.
- When starting a new experiment, sketch a block diagram of the apparatus and signal chain.
- Record extensive narrative of your experimental work, in and out of lab. Describe what you did, why you did it, what you saw, and what you did next. Note typical instrument settings so as to be able to quickly set up an experiment on subsequent days. Sketch waveforms at various places within the signal chain. This will help ensure your understanding of each component and permit you to rapidly identify equipment failure.
- Tabulate data into columns with headings, units, and estimated measurement uncertainties. Tables of raw data are the core of your notebook, but it must be more than just a data log.
- Identify the location of large data files or long analysis programs if they are too big to directly enter into your notebook.
- Don't wait until after the lab session has ended to visually examine the quality of your data. Create hand drawn plots of data with error bars as they are acquired, not later. These initial plots will inevitably save you time and frustration in making sure that your data are reasonable and suggestive of the behavior you expect. The importance of making preliminary plots and analyses in real time cannot be overstated.
- Your notebook should contain your analysis, results, and conclusions. These should be documented with narrative, formulas, computations, plots, and error estimates, just like in-lab work. Remember to annotate graphics with as much information as possible about how they were created. Bring your notebook to every lab session and to all oral exams. Failure to do so may result in penalties to your grade!
Project teams must create a 30”x20” poster to display at our open house on the last day of classes. Submit an electronic copy of the poster to Stellar in PDF format.
The lab is located in room 16-352. Based on sign-ups on the reservation calendar, the lab may be open:
Please make sure to reserve a lab station on the reservation calendar at least 24 hours in advance to ensure that an instructor will be present to open the lab. Contact one of the instructors if you would like to schedule lab work outside of the normal opening hours. Special lab sessions and weekend hours will be announced on Stellar.
The course Stellar site (20.345 Stellar) has an exhaustive list of assignments and due dates.
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