Physics 131 Reminders from 3/13 TA & LA Training (for week of 3/23 Lab 3, Part 1)

Hello!

Before you run lab & recitation this week, we wanted to give you a few reminders.

1) Recitation: either Electrophoresis (Wed/Thurs Sections) OR Electric forces exam problem.pdf  & Hydrogen bonding I (Mon/Tues Sections)

(Remember that recitation and lab are no longer aligned.  It's a Mad, Mad, Mad, Mad World!)

For those sections working with "Electrophoresis":

(And check out that cool image of gel structure linked below!)

(It might help students if you discuss, after the recitation has concluded, the power of a 'null' result.  Finding out what doesn't work or that a conclusion can't be made is often as powerful (i.e., instructive, generative) as finding something that works!) 

From Ben Geller, Oct. 2013: "So Vashti and I spent an hour talking about electrophoresis after I talked to you guys today.  We were tying to figure out exactly what agarose looks like at the microscopic level.  There's a pic on this page:

http://ocw.mit.edu/courses/biological-engineering/20-109-laboratory-fundamentals-in-biological-engineering-spring-2010/labs/module-1-day-2-purify-aptamer-encoding-dna/

So basically, the little stuff gets through this mesh-like gel more easily than the big stuff. :)

This might be a pic you want to show the students in recitation if, by the end of the hour, they are wondering what the gel actually looks like."

(break; Pass back Lab 2, if graded....)

2) Lab 3, Part 1: Random Motion and Diffusion (Labs now in room 3310!)

Link to documents & sample video and Excel analysis file: http://umdberg.pbworks.com/w/page/68933700/NEXUS%20Physics%20Labs%2C%202013-2014 (The sample Excel file is also attached to this email.)

Background readings that might help:

Modeling Fluids at the Macro-, Micro-, and Mesoscales

Coherent vs random motion (2013)

Diffusion and random walks (2013)

The role of randomness: Biological implications (2013)

Notes:

a) EQUIPMENT:

The lab equipment is all nicely prepared, including the solutions for all videos.  All of the vials are individually labeled, including the bead size, the bead material (Silicon or Polystyrene), and the solution type (Water, Low Glycerol = 15%, and High Glycerol = 30%).

All vials have been checked and contain viable solutions.  Remind students to shake the vials before extracting the solution with the micropipettes.  Students should use only a very small amount of each solution, so these vials should be more than sufficient for the full week of labs, all sections included.  Please put the vials back where they belong and refrigerate them between lab sections.

Plastic tips and slides are located on the top and next-to-top shelves in the center-left back cabinet.  Each group will need 4 tips (one for each of the three solutions and a spare in case they need to re-take a solution and have forgotten which tip to use).  These should be disposed of at the end of the lab (in the trash) and replaced for the next lab group.  Each group should only need one glass slide--as long as the samples placed on the slide do not touch, the same slide can be used for all three videos, even if they need to repeat solutions.  Used slides should be placed in the red container on top of the refrigerator.  (Do NOT slide the cover of this container closed all the way, as it will lock tight.)  Some videos may need to be taken twice or other solutions prepared, so a single lab group might occasionally need a second glass slide--but they should need no more than two. (I checked all of the solutions that Don prepared--all nine--on a single glass slide without having the solutions overlap.  They can get quite a lot of mileage out of a single slide.)  After you give the students their slides, PLEASE be sure to RE-COVER the box of slides (put the lid back on)!  Also, be sure to give the students the SAFETY INSTRUCTIONS for using these delicate glass slides.

Don't forget to check that all microscopes have been turned off after the videos are collected/before you leave lab.  The bulbs on these scopes are quite expensive and we are trying to prolong their life/use.

b) Sample Lab Reports

Some TAs expressed a desire to see some sample lab reports from two years ago for this lab.  I have attached a set, including some sample data.  Week 1 is essentially Lab 3 from that year, and weeks 2 and 3 are essentially Lab 4 from that year.  This may help you get a feel for what the students can accomplish.

c) Tricks for getting good videos

0. Do NOT use cover slips for any of these solutions.

1. The students should all be using the 40x optic, and the 1024 resolution is best.  Calibration slides for finding the distance-to-pixel ratio are in the 'my documents' folder, in a 'calibration' folder.  For these calibration slides, the '0' and the '1' are separated by 100 microns.  You will also find images of yeast, 1 um beads, and 2 um beads, as captured by the microscope.  Students can use these as comparison to see that they have focused their microscope properly.  Since we are not giving them live yeast solutions this year, have them simply look at the images to see that the yeast and beads are of similar size and then qualitatively describe their first solution (before capturing video of that solution and beginning the analysis).  The AVERAGE FRAME RATE from VirtualDub must be recorded for EACH video taken--this data cannot be recovered after the next action in VirtualDub is taken and ImageJ is NEVER correct about timing.

2.  Due to the depth of the liquid sample (drop of fluid), the microscopes can actually focus across a wide range.  Students want to focus as close to the glass slide as possible.  Focusing close to the upper surface of the 'drop' can result in a shaky/vibrating image.  Students may also get a vibrating image if anybody in the group is touching/bumping the desk under the microscope.  Focusing in the middle of the drop can be problematic for automatic tracking as beads moving vertically will pop in and out of existence in the microscope's horizontal plane of view.

3. If the samples on the slide are left over the hot bulb of the microscope for too long, convection currents can create directed motion in the fluid, moving the beads in a non-random fashion.  So videos should be taken fairly soon after the slide is placed on the microscope (or soon after the drop is placed on the slide).

4.  On the down side, ANY beads in a glycerol solution (low or high) will take some time to settle out against the glass slide, where there will be a high enough population to analyze.  So, after the glycerol solutions are deposited on the slide, the students should wait a minute or so to gather the video (and the slide should not be over the heated bulb for this waiting time).

5. Only video 1 will be analyzed in Part 1--so videos 2 and 3 should be SAVED to a flashdrive/email account/dropbox, etc..  Students have been reminded to bring their flashdrives.

d) Tricks for speeding up data analysis

1. After the video has been capture by VirtualDub, students can copy the file to the other desktop computer.  Now, analyzing this video file on TWO computers, students can track beads in different halves of the video (one computer does the agreed upon frames for beads on the LEFT side of the video and the other computer does the agreed upon frames for beads on the RIGHT side of the video).  This cuts the data collection/'harvesting' time in half for the 30-50 beads needed to create good histograms.  Students should not track 'stuck' or 'clumped' beads.  Help the students make a judicious selection of equally-spaced frames for tracking from the total frames imported into ImageJ.

2.  After the data has been 'harvested' using ImageJ, students should combine their data into a single Excel file.  They should make a BACK-UP COPY of their data before beginning to manipulate with Excel.  They should also PLAN AHEAD before trying to do the analysis.  Planning ahead will save them a lot of frustration and wasted effort.  (You can practice the steps you think are necessary on the sample data file attached to this email.  Remember, there is not one single way to perform the analysis--so don't lecture your method to the students once you decide what you think is best--but the students should think through a plan to get the from the raw data to the information they will need for the averages and histograms.)

3. Once the data file is at the delta x, delta y, and r stage for all beads, the file can again be split onto two computers so that the histograms can be produced more rapidly.

e) Group Rotation / Lab jobs (if using them)

For this new lab, please rotate the student groups (mix up the group memberships). Students should have new jobs for this three week lab.

3)  Other Logistics Stuff

a) Task for next training: To help you get a feel for how to help your students this week and in the coming weeks, please take some time to think through the steps you would need to do (or the questions you would need to ask yourself) in order to perform an ImageJ data harvesting on a generic video.  Please do the same task for performing an Excel analysis on generic data.  Making sure that you have these ideas clear in the abstract will aid you in guiding/helping your students in a concrete example.  We will take some time of Friday to generate these lists in small groups, but you should be thinking about it independently beforehand.

b) Don't forget to clean the lab up and leave it in neat shape for the next lab group.  You can make your students do most of the work--just give clear instructions!

c) Collect the recitation documents during the break between recitation and lab.  Place these at the back by the printer.

d) Make sure the lab documents don't get all mixed together.  Place these neatly at the back by the printer.  Old technical documents (like the Excel and ImageJ Intros) are in the wire paper holder by the printer.

e) If solutions run low or you are having computer troubles, see Don or Bill.

That should do it for this week!

~KIM