20.109(S12)

Welcome and Details for Spring 2012

Lecture: T/R 11-12 (4-237)
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 many 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.

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.

Announcements

• Hi folks - I will be holding office hours ~ 5:15 (maybe 5:20) today as planned, till about 6 pm. AgiStachowiak 17:05, 13 March 2012 (EDT)
• One more: in some cases, calculated %-ages do not appear to match the curves posted. One option for reminding yourself how linear interpolation works is Google. Good luck all, and hope to see many of you tomorrow!
• Sunday announcements AgiStachowiak 21:14, 11 March 2012 (EDT)
  • The company and exact name of the kit you used for RT-PCR is now posted in that day's Reagent List. Do read the ingredients and remember to describe those unique to your experiment.
  • Thanks to most of you for posting your data. I know some of you are still trying to figure it out, and hopefully I can help over email or in person, or your peers can. Please at the very least upload your raw data curves (or your corrected ones, if you have those) so everyone else knows whether your data looks robust or your curves are oddly shaped. Use the "upload file" option in the toolbox at the left-hand side-bar of OpenWetWare and copy the syntax that your peers have used.
  • Note that the page lengths we have suggested for the report are somewhat arbitrary and abstract. Thinking more about the specific content of your report, I'd say the Results guideline is on the high side (~3 is good), and for Discussion although 4 pages is not impossible please remember that more is not necessarily better. The 3-4 page guideline accounts for different writing styles, possibility of using sub-section titles, etc.
• Saturday announcements AgiStachowiak 13:33, 10 March 2012 (EST)
  • To allow analysis of class-wide trends, please post your binding data by 5 pm today (T/R section), or at the very latest 5 pm tomorrow (W/F section). Keep the following in mind:
    • To give others a sense of the quality of your data, you are strongly encouraged to post an image of your corrected absorbance curves a la the spring 2011 page.
    • Be thoughtful about significant figures in the data you post. Do not state far more precise numbers than you can believe. (One or two extra digits, please.)
  • Office hours will be held tomorrow, Monday, and (I hope) briefly Tuesday. Times are listed below. Hope to see many of you there!
• Hi all. Just a reminder that journal clubs today start at 1:30 sharp, and tomorrow begin at 1:10 sharp. AgiStachowiak 10:17, 8 March 2012 (EST)
• W/F binding assay data is posted on the Day 7 Talk page. AgiStachowiak 16:29, 7 March 2012 (EST)
• T/R binding assay data is posted on the Day 7 Talk page. AgiStachowiak 16:40, 6 March 2012 (EST)
• W/F section: Marilee's comments on your exercise from Wednesday's workshop will be available for pick-up at office hours. (Results or figure revision, that is.)
• Module 1 Office Hours Schedule. All will be held in 16-336.
  • This Monday, March 5th, 3-4 pm.
    • Note that I am unlikely to have all the homeworks graded by 3 pm, but I will have looked at enough of them to give some verbal feedback to whoever shows up.
  • Next Sunday, March 11th, 1:30-3pm; that Monday 3-4:30 pm; tentatively that Tuesday 5:15-6 pm, lab work allowing and if absolutely necessary.
• M1D5 RT-PCR gels for the W/F section are posted on the Talk page. I apologize that I forgot to post these sooner. Jacob will post the sample order shortly. Everyone got tons of product for at least one of their two samples, great job! AgiStachowiak 12:09, 2 March 2012 (EST)
• M1D5 RT-PCR gels for the T/R section are posted on the Talk page. Everyone got tons of product, great job!
• A couple of small clarifications have been made to the FNT due on Mod 1, Day 5. AgiStachowiak 15:17, 24 February 2012 (EST)
• There were two errors (out-of-date information) in the Day 2 reagent list that are now fixed. Please look again at the DNA purification kit and the gel stain that you used. AgiStachowiak 16:19, 22 February 2012 (EST)
• The journal club paper list is (belatedly) updated. Sign up away! Please note the requested sign-up format to use (colored letters, etc.); you can copy and modify the code in the Logistics section as needed. AgiStachowiak 15:51, 21 February 2012 (EST)
• Lecture/pre-lab notes for M1D2 have been posted; sorry I forgot about those yesterday! Fyi, one way to always know when they are up is to "watch" the Schedule page. AgiStachowiak 10:41, 15 February 2012 (EST)
• Test announcement for "watch" settings. AgiStachowiak 13:21, 13 February 2012 (EST)

• You can find old announcements here