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20.109(F12): Laboratory Fundamentals of Biological Engineering

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Fall 2012

Instructors: Angela Belcher, Bevin Engelward, Shannon Hughes-Alford, Natalie Kuldell and Agi Stachowiak
Writing Instructor: Leslie Ann Roldan
Oral Presentation Instructor: Atissa Banuazizi
Graduate TAs: Jenny Kay, Eric Ma, and Jackie Ohmura

Lecture: T/R 11-12 (16-220)
Lab: T/R 1-5 or W/F 1-5 (56-322)
Seminar Room: 16-336

Welcome to 20.109! For many of you this will be the first time in a research lab and for others it will not, but it is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. There is not time enough to show you everything you’ll need to know if you go on to do research, but after taking this class you should feel confident and familiar with some fundamental experimental approaches and lab protocols. You will develop good habits at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of the semester, you should also be aware of good scientific practice, having had some experience with report writing, notebook keeping and publicly presenting your data. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

  • To submit your major assignments, access the Stellar drop-box that's here


  • Please post your flow cytometry results on the M1D7 Talk page if you haven't already. It's great to see trends emerging from the data that has been posted so far, but the more data we have, the better we can draw statistically meaningful conclusions. Thanks! AgiStachowiak 15:46, 9 October 2012 (EDT)
  • NK office hours on 10.9.12 will be from 10:30 to 11:30 in the lab, 56-322.
  • The blog site is not allowing all users to log-in. If you have this problem, please just email your blog post to NK and it will be posted to your blog account once the site's hiccups have gone away. Thanks!
  • As was announced in class last R/F, you WILL be allowed to have your pre-lab notes at the second lab certification, in addition to your laboratory notebooks (including the primer design document). Please see the revised assignment instructions here. AgiStachowiak 10:22, 1 October 2012 (EDT)
  • NK office hours on 10.1 will be 10:30-11:30 in the lab.
  • The schedule for the FACS data analysis defenses with Bevin will be in 56-711 at 2:30-2:50, then 2:50-3:10 on Thursday 10.11.12 or in 56-202 at 4:00-4:20, then 4:20-4:40 on 10.12.12.
  • W/F lab: Your diagnostic gels have joined T/R's on the Talk page for M1D5. I'm happy to discuss results at office hours.
  • T/R lab: Your lovely diagnotic digest gels are now posted to the Talk page for M1D5. Check out your results and ask if you have any questions about what you see!!
  • For Tuesday's lecture (10.2) please read the Rad51 paper up until the bottom of the left column on page 601 and study figures 1-3. The Rad51 paper is linked from the front page of the DNA Engineering module.
  • Agi's current office hours schedule will always be posted on the Talk tab of her user page, linked here. This coming week, Monday office hours will be held from 12:30-1:30 (I have a one-time conflict at the usual 2-3), and Tuesday office hours from 4-5 pm. Note that I'm happy to answer questions about optional homework assignments that you have tried.
  • I've just posted my M1D3 notes -- with apologies for forgetting to do so before traveling this weekend. Consider putting a "watch" on the Schedule page to always know when lecture notes have been posted. Hope to see some of you at office hours this afternoon! AgiStachowiak 12:13, 25 September 2012 (EDT)
  • Since a few people have had trouble locating the gels I ran after class last week, the link to them is here. You can also reach this page by going to the M1D3 page and then clicking the "talk" link at the very top of the page.
  • Hi all -- for this week, Agi will have office hours from 4-5 pm on Tuesday, in 16-319. Future OH will be some combinations of Mondays 2-3 pm and Tuesdays 4-5 pm (some weeks both days).
  • Hi all -- for this week, Agi will have office hours from 2:30-3:00 pm, in 16-319. Future OH are TBD, pending more responses to the poll.
  • Hi folks -- just a reminder that Agi's office hours poll is linked at here. Please fill out tonight if you can!
  • NK office hours will be Mondays from 10-11 in lab, starting Monday Sept 24th.
  • A note about quizzes: The material will be primarily based on 1) the previous lecture and 2) the lab introduction material (with perhaps some minor questions from the protocol) of the lab you are about to complete. For example, your quiz on M1D2 will be regarding the material given in the M1D2 introduction and the M1D1 lecture.
  • There will be no student written quiz on Tuesday/Wednesday of this week (9.11 and 9.12) since we'll be having a Lab Certification. Quizzes will start on Thursday/Friday of week 1and you should assume there will one every day EXCEPT the first day of a new module OR a day there is a Lab Certification.
  • You will need your lab notebooks on Tuesday/Wednesday (9.11 and 9.12) to record the work you do at the very end of lab.
  • For Tuesday's lecture (9.11), we will have the LateNiteLabs folks visiting and they will walk through the virtual lab environment. If you have a laptop that you can bring to lecture on 9/11, you might enjoy walking through the labs with them on your own computer.
  • Please check out the Assignments link so you and your lab partner can make your choices no later than M1D3.
  • 20.109(F12): Quick Facts
  • You can find old announcements here
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