Gas station without pumps

2018 April 13

Spit kit sent

Filed under: Uncategorized — gasstationwithoutpumps @ 09:22
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I sent in my spit kit (formally “ORAgene⋅Dx For collection of human DNA”) to Dante Labs for whole-genome sequencing (WGS) for myself yesterday, as the next step after ordering the sequencing as mentioned in Personal genome sequencing.

I expect that it will take about 3 months before I have any data from them, as they are not paying for quick turnaround from the sequencing labs, and even quick turnaround would be a couple of weeks with the low-cost sequencing methods.   Sometime this summer I’ll either be posting some (limited) information about the results or complaining about a scam—we’ll have to wait and see.

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2018 April 4

Quiz disappointment

Filed under: Circuits course — gasstationwithoutpumps @ 22:31
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Today’s quiz in class was very disappointing for me, and I don’t know what to do differently to get better results.

Yesterday in lab I returned the quizzes from before break and urged students to look through all the old quizzes and rework any questions they got wrong, reminding them that I recycle questions.

In this morning’s class, before the quiz students asked me to show them (again) how to do one of the questions on the last quiz:

Design a voltage divider implementing Vout − Vref = G(Vin − Vref ), where G can be adjusted from ≈ 0.33 to ≈ 0.67 using a 10 kΩ potentiometer. Use port symbols to connect to Vin, Vref , and Vout.

I showed them two solutions—one that I had expected and a correct, but different solution that a student had come up with.

Here are the two solutions: mine on the left and an alternative one on the right.  (There is a third solution, similar to the second one, but with the potentiometer as variable resistor on the lower leg, rather than the upper one, and the two fixed resistors swapped.)

I had already shown them my solution a week and a half ago, right after they took the quiz, and I had posted both solutions on Piazza.  I not only showed the solution, but gave them an explanation of how it worked again and answered some questions students had about it (like why the gain was expressed the way it was with Vref, and why it was even considered a gain).

Right after that I erased the board and handed out the quizzes.  One of the quiz questions was the identical question that I had just worked on the board for them.  I was resigned to this being a free point for them (just like putting their section number on the quiz is a free point, which I use to distinguish those who are absent from those who are present but get no questions right).

But 20 of the students got no points for the question and 15 got only half credit (out of a class of about 72—there were supposed to be 79, but there were 7 students absent).  So almost half the class could not retain for 5 minutes a simple circuit that they should have been able to derive in a couple of minutes and which they had seen at least 3 times already.

Help!  During the last 10 weeks I’ve gone through just about all the ways I can think of to have the students understand voltage dividers and potentiometers, and I’m obviously not getting through to 28% of them (probably more, since the absentees are likely to be in the group that can’t do the problem also).

Does anyone have any useful advice?  (Giving up on the students is not useful advice—I want them to succeed.)

2018 April 1

Starting new quarter

Filed under: Circuits course — gasstationwithoutpumps @ 17:20
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Tomorrow the new quarter starts, and I hardly feel like I’ve had a break—I was grading continuously through Monday, working on my book through Friday, and setting up Canvas with all the assignments today. I also spent several hours this week reading course syllabi and student petitions for the Committee on Courses of Instruction meeting that is tomorrow afternoon and a little time reading senior thesis proposals from students wanting to start senior theses next quarter.

It probably doesn’t help that I’m on the third week of a cold—it has settled down to being a minor cough, but it is still making me more tired than usual and interfering with my sleep (the cough is worse when I’m lying down).

There is a new draft of Applied Electronics for Bioengineers posted—those who have already bought the book should have gotten an e-mail about the free update.  The minimum price for the book has gone up by 1¢, as Leanpub now has a $5 minimum, and I had set my book at $4.99 minimum.  There are not many changes this time, because I did not have a lot of writing time last quarter:

  • Beefed up the chapter on lab report guidelines.
  • Many typo and minor wording fixes (mainly ones reported by students in class).
  • Replaced Waveforms 2015 references with Waveforms 3, due to name change by Digilent.
  • Added paragraph to thermistor lab about doing design around standard parts.
  • Also added specific discussion of using parallel resistors for current sensing in power-amp lab.
  • Added the missing section on high-pass active filters.

By being somewhat generous on my grading for the final lab report, I managed to keep the number of failures for Winter quarter down to two—one flaked so much that all five labs had resulted in the partner requesting doing separate lab reports and the other did not do the last lab.  This is about the usual failure rate (2–3%). Still, I was not happy with how many C grades I had to give—I’d like to see a higher distribution Spring quarter.

Several of the students in my course had previously taken EE101 (circuits) or were taking it concurrently.  I checked, and there was essentially no correlation between the EE101 grade and the grade in my course (Kendall tau correlation about -0.03 for not-taking/taking and +0.07 for grade among those who took—neither is a statistically significant relationship with p-value>0.64).

I think that what would make the biggest difference in the grades is better writing from the students—many of the lab reports were a struggle to get through, with poor organization, poor paragraphing, poor grammar, poor word choices, poor punctuation, and poor formatting.  Only about 10% of the class was writing at a level I would consider acceptable for college students, and I’ll be stressing writing more in Spring quarter.

Having undergrad graders in Spring quarter rather than a TA may help, as I have a couple of very competent undergrads who can provide writing feedback on the prelab assignments in a timely fashion.  The foreign TA I had last quarter took a long time getting feedback to students and was not really able to provide writing feedback—not a bad TA for an EE course, but not up to the heavy grading demands of this course.  The graders will be grading the homework and the prelab assignments, but I’ll still be grading the quizzes (which only take about 2–3 hours a week to grade) and the final lab reports (which will take about 150–200 hours to grade for the quarter).

The grading last quarter was stressful, and I expect it will be again this quarter.  Grading at home during finals week resulted in me putting on five pounds—I kept rewarding myself with snacks after getting through another couple of papers.  I’m hoping that I can get the students to write a little better and a little more tersely this quarter, so that the grading will be less stressful (and I can take the weight off again).

I’m hoping that I can convince more of the students to get out of answer-getting and point-scoring mode (see Just scoring points) on the quizzes and rework any problems they get wrong—I’m tired of asking essentially the same question in quiz after quiz and having students still miss it.

2018 March 29

Regrowth: a return to normal

Filed under: Uncategorized — gasstationwithoutpumps @ 17:04
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As those who’ve been reading my blog for the past five months know, in October I had my head shaved as part of a fundraiser for pediatric cancer research, including my beard and my eyebrows.  (I believe that it is still possible to donate at https://www.stbaldricks.org/participants/Karplus2017.)

Since then, I’ve had a photograph taken about every two weeks, to record the regrowth of my beard and head hair, and my gradual return to a normal (for me) appearance.

Before getting shaved, this is what I looked like.

This is what I looked like right after the shaving, wearing the silly medal they gave me for the most funds raised at UCSC for St. Baldrick’s.

After 2 weeks there was some grey stubble on my chin and shorter brown stubble on top of my head.

After 4 weeks the grey beard began to look like an unsuccessful attempt at growing a beard, rather than just stubble.

After 6 weeks, the beard looked deliberate, but the hair on top of my head still looked like it had just been shorn off.

At nine weeks the beard looked more or less normal, though about as short as I’ve ever trimmed it. The pattern of white and dark hair in the beard stands in strong contrast to the uniformly dark hair on top of my head.

At eleven weeks, I dyed the beard to make the color contrast less, shaved my cheeks, and trimmed my mustache.

At thirteen weeks the beard looked ok, if a little scruffy and the head hair was starting to come back, though the “reverse Mohawk” stripe from front to back where they had shaved closer was still visible.

At fifteen weeks the beard dye was fading out (I use a dye that gradually washes out).

At seventeen weeks I had re-dyed the beard to match my head hair.

At 20 weeks the beard was pretty much back to normal (though still substantially shorter than what I started with), and the head hair was getting close to where I have it cut to at the beginning of a summer.

At twenty two weeks after the shaving, I re-dyed my beard yet again, in anticipation of the start of a new quarter. I expect to dye the beard about every 8–12 weeks, to keep it more or less coordinated with the hair on top of my head, instead of the white with darker stripes that can be seen in weeks 4–9.

2018 March 28

Personal genome sequencing

Filed under: Uncategorized — gasstationwithoutpumps @ 12:41
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I have just ordered whole-genome sequencing (WGS) for myself from Dante Labs, as I suggested I would do in Direct-to-consumer genome sequencing.

Dante Labs has the cheapest WGS service I could find at $499.  They say that they ship the data in 3 forms: FASTQ, BAM , and gVCF.  The FASTQ format is basically the raw read information from the sequencing machine, BAM is the alignment of the reads to a reference genome, and gVCF is a variant-call file based on the alignment of the reads to the genome.

Many other sequencing services charge extra for sending you the data, as they want to hang onto it and charge ridiculously large amounts to run little software genetic tests on it.  You can get essentially all the standard tests run on the data by Promethease for about $10.  The Promethease analysis is limited to what is in the SNPedia database, which is a fairly large database of published information about genomic variation, with pointers to the original literature.

I’m interested in finding out what my inherited bradycardia (resting heartbeat lower than 60bpm) stems from. The inheritance of this condition has not been studied much as it has little medical consequence by itself (an increased need for pacemakers in old age, perhaps).  Most bradycardia is caused by heart damage and old age, so that is what gets studied.

I found a good open-access survey article on the subject,

Inherited bradyarrhythmia: A diverse genetic background
Taisuke Ishikawa, DVM, PhD, Yukiomi Tsuji, MD, PhD, Naomasa Makita, MD, PhD
Journal of Arrhythmia 32 (2016) 352–358

in which 16 genes are linked with bradycardia (though often with serious other conditions, which our family does not have).  SNPedia only mentions bradycardia 8 times (talking about only 3 genes), and there is no overlap between SNPedia’s entries and the genes in the survey article, so it is clear that SNPedia is not going to be very useful here.

I believe that Dante Labs uses SNPeff to do its annotation, a free tool that seems to be even older and less up to date than Promethease’s use of SNPedia.  But I don’t think that any of the commercial services will be any better for the analysis I’m interested in, as it is quite likely that my family has an idiosyncratic mutation that has not been published.

I’ve communicated with Dante Labs, and they say that the $500 produce is for 30X sequencing with BGI sequencers (not Illumina).  I was worried that the price was too low to be real, as even wholesale sequencing for large numbers of genomes is $600 each from BGI, but a couple of people in Europe that I communicated with were pretty sure that Dante Labs was a reputable lab, and one said that he’d run 10 genome samples through them.  I was reassured enough to risk the $500 on testing my own genome, but I’ll wait until that data comes back before testing anyone else in the family.

I expect that it will take 3 or 4 months before I have any data from them, as they are not paying for quick turnaround from the sequencing labs, and even quick turnaround would be a couple of weeks with the low-cost sequencing methods.

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