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20.109(S14): Laboratory Fundamentals of Biological Engineering

Feliks signaling-network-crop.jpg

Home        Schedule Spring 2014        Assignments       
Module 1        Module 2        Module 3              

Welcome and Details for Spring 2014

Lecture: T/R 11-12 (16-220)
Lab: T/R 1-5 or W/F 1-5 (56-322)
People: Instructor and student web pages may be found at the linked People page.

Welcome to 20.109! For some of you this will be the first time in a research lab and for others it will not; either way, 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 data and your ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

Cover image: Is it a biological signaling network or a toddler's whiteboard scrawlings?

Orientation and Safety Material

On the first day of 20.109, you will take an interactive tour to get up to speed on the basics of working in a lab. The lab tour is linked here. You should also carefully read the general lab policy, which broadly covers dos and don'ts specific to our class.

Later in the semester, you will want to read guidelines for working in the tissue culture facility. Stay tuned!

At any time you can refer the guidelines on using personal protective equipment developed by the Environmental Health and Safety Office (EHS) at MIT: one on eye protection (PDF download) and one on wearing lab coats (PDF download).

Finally, you can learn how to best contribute to the class wiki at the linked OWW in 20.109 page.

Office Hours Schedule

  • Ongoing:
    • Shannon: Monday 12pm (16-429b) and Monday 9pm (lab, 56-322)
    • Agi: Monday 1:30-2:30 pm (16-319)
      • CANCELLED Monday 4/14 (see below)
  • Additional:
    • Module 1 data summary
      • Agi: Sunday Mar 9th 1:30-3pm (56-322); Monday Mar 10th 1-2:30 pm (56-322); also Tuesday Mar 11th 3:30-4:30 pm (16-336)
      • Shannon: Sunday Mar 9th 3:30-5pm (56-322); Monday Mar 10th 4-6pm & 9-10pm (56-322 or near there)
    • Module 1 memo
      • Agi: extended time and bigger room on Monday, 1:30-3 pm (56-322); also Tuesday, 9:30-11 am (16-319)
    • Module 1 summary rewrite
      • Shannon: Wednesday Apr 2nd, 12pm (16-429b); Thursday, Apr 3rd 10am-11am (16-429b)
      • Agi: Thursday Apr 3rd, 9am-10am (16-319)
    • Module 2 research article
      • Agi: Thursday 4/17 at 4-5 pm (16-319 or 16-336, TBD); Sunday 4/20 at 2-3:30 pm (56-322); Tuesday 4/22 at 4-6 pm (56-322)
      • Shannon: Friday, 4/18 at 3-5 pm (16-429); Sunday 4/20 at 3:30-5 pm (56 3rd floor lunchroom); Tuesday 4/22 at 1-3 pm (56-302) & 3-4pm (56-322 or lunchroom)
    • Module 3 research proposal
      • Agi: By appointment is usually most effective for this assignment. I'd love to discuss your projects with as many of you as are interested! I may put out a Doodle sign-up if demand is high (versus coordinating individual emails). Note that I will be attending the T/R M3D8 talks and will not be available then.
      • Shannon: Saturday, May 10th -- Noon - 2pm in 56 3rd floor lunchroom. Normal Monday OH.


  • The W/F qPCR data and images are now posted on the Talk page. Both TR and WF folks are welcome to look at the cross-plate replication study we ended up doing for WF Yellow Team when their co-super-group-member's samples were not ready for the original qPCR run. AgiStachowiak 15:04, 6 May 2014 (EDT)
  • M3D6 is in final form, and T/R qPCR data and images are posted on the Talk page. (W/F data and images will be posted sometime tomorrow afternoon, including the extra run for Grn/Ylw.) AgiStachowiak 12:22, 5 May 2014 (EDT)
  • A few clarifications/minor edits were made to the proposal presentation assignment description. See the history tab or ask Agi for details. AgiStachowiak 15:58, 30 April 2014 (EDT)
  • M3D5 and the mini-report description are now in final form. AgiStachowiak 11:07, 29 April 2014 (EDT)
  • Transfer buffer composition had been missing from the M2D2 Reagent List – fixed now, sorry! AgiStachowiak 14:07, 20 April 2014 (EDT)
  • Please note the change to the M3D3 FNT. Also, remember that this day happens in shifts: don't forget to sign up for a time on the M3D3 Talk page. AgiStachowiak 21:55, 16 April 2014 (EDT)
  • The M3D1 wiki page is now revised for the current semester. AgiStachowiak 15:36, 9 April 2014 (EDT)
  • The final version of the M2D6 FNT is now up, and ditto for the Reagent List. The research article assignment description will be revised/filled in shortly. Thanks for your patience! AgiStachowiak 10:43, 5 April 2014 (EDT)
  • The M2D6 intro is now in final form (just a couple tweaks for comprehensibility), as is Part 1 of the protocol (includes important change to table!). Part 2 of the protocol is a work in progress, as is the FNT and Reagent List… AgiStachowiak 15:32, 2 April 2014 (EDT)
  • Aneesh has made a lovely visualization of the Day 5 workflow. Check out the updated protocol! AgiStachowiak 13:45, 31 March 2014 (EDT)
  • The M2D1 FNT and Reagent List are now up to date. AgiStachowiak 16:07, 11 March 2014 (EDT)
  • As we hope you all picked up on via email, the M1 microbiota summary is now due Wednesday, March 12th at 1 PM for everyone.
  • Hi folks! The M1D6 FNT has been revised to include some reminders (reflections and notebooks). Relatedly, M1D7 Part 1 is now fully revised. AgiStachowiak 11:05, 1 March 2014 (EST)
  • Prof. Runstadler has graciously shared his outlines/notes for the lecture parts done on the blackboard. These are available as DOC/DOCX on the Schedule page, so you can add your own annotations. If you would like a PDF copy, please email an instructor. AgiStachowiak 09:17, 24 February 2014 (EST)
  • M1D4 announcements for W/F section:
    • You may retrieve your digital gel images on the M1D4 Talk page.
    • All the plates grew colonies!
    • All groups (except Pink) were plated between 6:25-6:35 pm on Friday, in the order: red, ylw, whi, sil, grn ,prp, org, blu.
  • The lab quiz dates are now all posted on the Schedule page. Please also see the lab notebook link for the possible notebooks that may be collected and their associated due dates. Thanks! -Agi
  • You can find old announcements here