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2015 April 23

Very long couple of days

Yesterday and today have been draining.

Yesterday, I had three classes each 70 minutes long: banana slug genomics, applied electronics for bioengineers, and a guest lecture for another class on protein structure.  I also had my usual 2 hours of office hours, delayed by half an hour because of the guest lecture.

The banana-slug-genomics class is going well.  My co-instructor (Ed Green) has done most of the organizing and has either arranged guest lectures or taught classes himself. This week and part of next we are getting preliminary reports from the 5 student groups on how the assemblies are coming.  No one has done an assembly yet, but there has been a fair amount of data cleanup and prep work (adapter removal, error correction, and estimates of what kmer sizes will work best in the de Bruijn graphs for assembly).  The data is quite clean, and we have about 23-fold coverage currently, which is just a little low for making good contigs.   (See https://banana-slug.soe.ucsc.edu/data_overview for more info about the data.) Most of the data is from a couple of lanes of HiSeq sequencing (2×100 bp) from 2 libraries (insert sizes around 370 and 600) , but some is from an early MySeq run (2×300bp), used to confirm that the libraries were good before the HiSeq run.  In class, we decided to seek a NextSeq run (2×250bp), either with the same libraries or with a new one, so that we could get more data quickly (we can get the data by next week, rather than waiting 2 or 3 weeks for a HiSeq run to piggyback on).  With the new data, we’ll have more than enough shotgun data for making the contigs.  The mate-pair libraries for scaffolding are still not ready (they’ve been failing quality checks and need to be redone), or we would run one of them on the NextSeq run.  We’ll probably also do a transcriptome library (in part to check quality of scaffolding, and in part to annotate the genome), and possibly a small-RNA library (a UCSC special interest).

The applied electronics lecture had a lot to cover, because the material on hysteresis that was not covered on Monday needed to be done before today’s lab, plus I had to show students how to interpret the 74HC15N datasheet for the Schmitt trigger, as we run them at 3.3V, but specs are only given for 2V, 4.5V, and 6V.  I also had to explain how the relaxation oscillator works (see last year’s blog post for the circuit they are using for the capacitance touch sensor).

Before getting to all the stuff on hysteresis, I had to finish up the data analysis for Tuesday’s lab, showing them how to fit models to the measured magnitude of impedance of the loudspeakers using gnuplot.  The fitting is fairly tricky, as the resistor has to be fit in one part of the curve, the inductor in another, and the RLC parameters for the resonance peak in yet another.  Furthermore, the radius of convergence is pretty small for the RLC parameters, so we had to do a lot of guessing reasonable values and seeing if we got convergence.  (See my post of 2 years ago for models that worked for measurements I made then.)

After the overstuffed electronics lecture, I had to move to the next classroom over and give a guest lecture on protein structure.  For this lecture I did some stuff on the chalk board, but mostly worked with 3D Darling models. When I did the guest lecture last year, I prepared a bunch of PDB files of protein structures to show the class, but I didn’t have the time or energy for that this year, so decided to do it all with the physical models.  I told students that the Darling models (which are the best kits I’ve seen for studying protein structure) are available for check out at the library, and that I had instructions for building protein chains with the Darling models plus homework in Spring 2011 with suggestions of things to build.  The protein structure lecture went fairly well, but I’m not sure how much students learned from it (as opposed to just being entertained).  The real learning comes from building the models oneself, but I did not have the luxury of making assignments for the course—nor would I have had time to grade them.

Speaking of grading, right after my 2 hours of office hours (full, as usual, with students wanting waivers for requirements that they had somehow neglected to fulfill), I had a stack of prelab assignments to grade for the hysteresis lab.  The results were not very encouraging, so I rewrote a section of my book to try to clarify the points that gave the students the most difficulty, adding in some scaffolding that I had thought would be unnecessary.  I’ve got too many students who can’t read something (like the derivation of the oscillation frequency for a relaxation oscillator on Wikipedia) and apply the same reasoning to their slightly different relaxation oscillator.  All they could do was copy the equations (which did not quite apply).  I put the updated book on the web site at about 11:30 p.m., emailed the students about it, ordered some more inductors for the power-amp lab, made my lunch for today, and crashed.

This morning, I got up around 6:30 a.m. (as I’ve been doing all quarter, though I am emphatically not a morning person), to make a thermos of tea, and process my half-day’s backlog of email (I get 50–100 messages a day, many of them needing immediate attention). I cycled up to work in time to open the lab at 10 a.m., then was there supervising students until after 7:30 pm. I had sort of expected that this time, as I knew that this lab was a long one (see Hysteresis lab too long from last year, and that was when the hysteresis lab was a two-day lab, not just one day).  Still, it made for a very long day.

I probably should be grading redone assignments today (I have a pile that were turned in Monday), but I don’t have the mental energy needed for grading tonight.  Tomorrow will be busy again, as I have banana-slug genomics, a visiting collaborator from UW, the electronics lecture (which needs to be about electrodes, and I’m not an expert on electrochemistry), and the grad research symposium all afternoon. I’ll also be getting another stack of design reports (14 of them, about 5 pages each) for this week’s lab, to fill up my weekend with grading. Plus I need to update a couple more chapters of the book before students get to them.

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