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2014 August 19

Two papers submitted

I got two papers with a co-author finished and submitted today.

One of them is based on the segmenter algorithms that I wrote up in this blog (with some improved parameterization): Segmenting noisy signals from nanopores, Segmenting filtered signals, and Segmenting noisy signals revisited.

The other one is an HMM paper that uses the automatic segmentation and an HMM that models the DNA motor behavior to do the same analysis that was done by hand in an earlier paper “Error Rates for Nanopore Discrimination Among Cytosine, Methylcytosine, and Hydroxymethylcytosine Along Individual DNA Strands” in PNAS.  The automatic HMM method was more accurate than the hand curation and feature extraction followed by sophisticated machine learning methods like support vector machines and random forests—I think that we were limited before by the biases of the hand curation and feature extraction.

Unfortunately, we were not able to do side-by-side comparison on exactly the same data, as the original data for the PNAS paper was lost in a 2-drive failure on a RAID that had not been properly backed up.

The paper writing did not take much of my time this summer, as my co-author did a lot of the writing and kept me from procrastinating too much.

I’ve also been working on my book, tentatively titled Applied Electronics for Bioengineers, but without a co-author to keep me honest, I’ve been doing a lot of procrastinating.  Yesterday I had planned to show the waveform of the gate signal on a nFET being used for pulse-width modulation, to show the “flat spot” that results from feedback through the gate-drain capacitance.  I fussed with that for quite a while, but never got a recording I liked the looks of—so ended up getting nothing written on the book.  I’ll probably try again tomorrow, but with a backup plan of working on a different section if that one gets too frustrating, or of writing some of the text that will go around the figure, once I get a figure I can use.

The book is currently 215 pages, but that includes the front matter and back matter.  The core of the book is only about 188 pages, with 74 figures.  I probably need a bunch more figures (schematics, graphs, photos, …), but those are what take the longest to produce.  There’s a little over a month left until classes start, but I don’t see myself finishing by then.

2014 June 14

Zeroth draft of book done

Filed under: Circuits course — gasstationwithoutpumps @ 23:02
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My big project for the summer is to convert my lab handouts and a few of my blog posts into a textbook: Applied Circuits for Bioengineers.

The first task was to take the existing handouts (each a separate LaTeX file) and merge them into a single book-style LaTeX document, with title page, table of contents, chapters, index, and all the other front matter and back matter of a book. I’ve now done that, making a crude split into chapters of background and “Lab” chapters.

The results are not very book-like in terms of content, but I now have a framework to which to add the missing background material.  I expect to spend a few hours a day on the book all summer, and somewhat less time on it in fall and winter, so that a complete draft will be ready for the next time I teach the course in Spring 2015.

I’ve not figured out how I will distribute the book when I’m finished—I’ll certainly be giving the PDF for free to students who take my course, but I’ve not decided whether to self-publish the book, work with a professional textbook publisher, work with an electronics hobbyist company, or just dump the book for free on the Internet.  Each has its advantages and disadvantages.

I’m producing the book using LaTeX—there is a fair amount of math and a lot of figures (64 so far, and probably many more to come), so no other tool I have available is suitable for producing a book-length document of this complexity.

One LaTeX problem I’m running into is that I want the lab assignments to be chapter level objects, but separately numbered from the chapters.  Currently I have the ugly approach of making the labs  be names of chapters: Chapter 9: Lab 4: Electret Microphones, which I’m really not happy with.  But changing the running heads and the table of contents entries is a bit tricky, particularly since some places use just the chapter number, which would have to be replaced by a word plus number.  I’ll probably play with things like getting interleaved lab and chapter numbering when I get too tired of writing content.

There will be some rather tedious parts to the writing—like adding index entries, which I may try to bribe my son or some students to do.

This zeroth draft of the book is currently 186 pages, with about 160 pages of content.  I expect the book to grow to about 240 pages of content as  I add more stuff from my lectures.

2014 June 12

Starting on book for circuits lab—scheduling labs

Filed under: Circuits course — gasstationwithoutpumps @ 23:59
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In Revised plan for circuits labs I provided a tentative schedule for the applied circuits course and lab, which I ended up not really following (dropping the FET measurements, moving the sampling lab after the loudspeaker lab, and swapping the order of the pressure sensor and the class-D amplifier).

I’m now trying to turn the course lab handouts into a book (which means adding everything that was previously just in lectures), and I’m trying to rearrange the lab schedule to fit better into the 10-week quarter and to flow a little better pedagogically.

In this post, I’ll ignore the lecture component, but just look at a possible reordering of the labs.  Squeezing the KL25Z soldering and both halves of the thermistor lab was too much, and the sampling and aliasing lab did not work well late in the quarter, so I’ll strip the filter design out of the sampling lab and simplify it a bit to get it in the first week, and move the thermistor lab fully to the second week.  I’ll have to squeeze somewhere else, and I think that the best bet is the hysteresis lab, which took far longer than it should have.  I still want to have data-analysis Wednesdays, and reports due on Fridays.

Tuesday week 1 Unpacking parts, labeling capacitor bags, using wire strippers, making clip leads, Soldering headers onto KL25Z boards, downloading data logger to KL25Z.See soldering instructions at Soldering headers on a Freedom board and Jameco soldering tips
Thursday week 1 Sampling and aliasing lab (no filter design)
Tuesday week 2 Measuring input resistance of multimeter, and of oscilloscope.
measuring thermistor resistance at many temperatures.
Thursday week 2 Measuring voltage of thermistor voltage divider, recording voltage vs. time.
Tuesday week 3 Measure I-vs-V DC characteristic of resistor and of electret mic, both with multimeter and with KL25Z board.
Thursday week 3 Look at mic with resistor load on oscilloscope (AC & DC coupling).  Filter design for AC coupling. Loudspeaker on function generator?
Tuesday week 4 Characterizing impedance of loudspeaker vs. frequency
Thursday week 4 Characterize hysteresis in Schmitt trigger chip using data logger. Breadboard hysteresis oscillator with various R and C values, measuring frequency or period (oscilloscope or frequency meter?).
Make and test touch sensor with breadboard oscillator. Solder hysteresis oscillator. Estimate capacitance of touch from change in period of hysteresis oscillator.
Tuesday week 5 Impedance of stainless steel (polarizing) electrodes in different NaCl concentrations (at several frequencies).
Thursday week 5 Impedance of Ag/AgCl (non-polarizing) electrodes in different NaCl concentrations (at several frequencies)
Tuesday week 6 Low-power single-stage audio amplifier with op amp
Thursday week 6 catchup day? characterizing photodiode or phototransistor?
Tuesday week 7 Pressure sensor day 1: design and soldering instrumentation amp prototype board
Thursday week 7 Pressure sensor day 2: further debugging.
Recording pressure pulses from blood-pressure cuff.
Tuesday week 8 Photodiode or phototransistor with single-stage simple transimpedance amplifier.
Freeform soldering to attach leads for fingertip transmission sensor.
Cut-and-try design for transimpedance gain needed to see reasonable signal without saturating amplifier. (Determine AC and DC components of current)
Thursday week 8 Fingertip pulse sensor with 2-stage amplifier and bandpass filtering.
Tuesday week 9 class D audio amplifier day 1(preamp and comparators) (problem with Memorial Day on Monday?)
Thursday week 9 class D audio amplifier day 2 (output stage)
Tuesday week 10 EKG day 1:  breadboard and debugging (confident students could go directly to soldering)
Thursday week 10 EKG day 2: soldering, debugging, and demo.  Last day for any catchup labs.

I’m not really comfortable with the class-D amplifier in the week with Memorial Day. I’ll have to double check when Memorial Day comes next year.

2014 June 2

What makes an award-winning senior project?

Filed under: Uncategorized — gasstationwithoutpumps @ 16:39
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I was on an awards committee for the School of Engineering this year, attempting to give awards to the best undergraduate projects.  The process is interesting, because the projects span a wide range of different disciplines and levels of sophistication.  We had faculty as judges whose fields were computer science, computer engineering,  biomolecular engineering, and technology management (no EE faculty this year). I was the “biomolecular” judge, though my training was in math and computer science and I taught computer engineering for over a decade before switching to biomolecular engineering.  I was probably the only one of the judges who was at least somewhat familiar with all the fields represented by the projects, which is the first main point:

An award-winning project has to be comprehensible to someone outside the group.
Not only does the project description need to state the design goal (or research question) clearly, but it also needs to provide a justification for why anyone would care. Several of the project descriptions seem to have been written solely for the head of the lab with no material to help someone from outside the lab understand what was going on. These were not award-winning—they may have been good research, but the presentation did not make that clear. The more esoteric the research, the clearer the statement to outsiders needs to be.

A good heuristic for student reports (at all levels from freshman essays to PhD theses) is to write to an audience of people who might be interested in joining the research group, but aren’t yet in that field or subfield. So a senior design report should be written with juniors in the same major as the main audience, with a somewhat more general intro and conclusion. If you learned something in the process of doing the project, you can’t assume that your audience has already learned it.


For some of the projects, I had a hard time figuring out what the students were trying to do and what they had actually done, which brings us to the next three points:

An award-winning project description starts with a simple statement of the design goal or research question.
I don’t want to read three or four pages of background about a field before finding out what the project is. Start with a simple statement of the problem in one or two paragraphs, then give the background, justification, or work by others needed to put it in context.
A thesis or student project report exists primarily to establish what the students have done.
I get tired of reading reports full of passive voice, in which things happen, but no one does things. I want to know who did what: what the students did, what was done by other lab members, what was purchased, what was done by collaborators elsewhere, and so on. For a senior thesis, which is a single-author work, there should be much more “I” than “we”, and the plural should only be used when the other people involved have been explicitly and unambiguously named.

A thesis is not about science or engineering, but about the particular contributions of a specific person to science or engineering. A senior design report may be a team effort (and so “we” may be more appropriate), but it is still mainly about what the team accomplished, not about the product they produced.

A project report must be specific and detailed.
In general, a thesis provided more detailed information than a journal paper, which in turn was more detailed than a poster, which was often more detailed than a set of slides. We tended to favor more detailed reports (whether single-author or multiple-author) over shorter summaries, and complete reports are better than proposals. Since the deadline for awards is earlier than the end-of-the-year deadline for design reports and theses, there is an enormous advantage to students who write as they do the work, rather than pushing the writing to the end of the project. (Students who write as they go also generally produce better writing and do better engineering, because they are not letting themselves get away with fuzzy thinking, but making sure that they can explain themselves every step of the way.)


Of course, no project can win an award unless good work is done, which brings us to the last point:

Award-winning work is carefully done as well as carefully described.
Engineering awards are given for good engineering, not for sloppy work full of obvious errors, nor for proposals that five minutes’ thought would show have no hope of succeeding. The judges may not be in your field, but they are engineers and they pay attention to details. There were several projects that I saw this year which raised red flags, and I spent a little time on Google searches or Wikipedia to check to see whether what the students said was reasonable. Occasionally, I found that I had a misunderstanding of a subject and I re-read the report with a corrected knowledge base. More often, I found that students hadn’t done even simple sanity checks that are apparent to people well outside the field.

Although I said above that a report is “mainly about what the team accomplished, not about the product they produced,” it is still essential to have a good description of the product, with detailed block diagrams, schematics, program pseudocode, or whatever other documentation is needed to communicate the design. The goal should be to have a report that could be handed over to a new team, who could then continue the project without much delay.

2014 May 21

Establishing the habit of writing

Filed under: Circuits course — gasstationwithoutpumps @ 09:19
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In Preparing for AP Physics 1: establishing the habit of writing Greg Jacobs writes

I’m in the infant stages of planning my AP Physics 1 course. The big trick is going to be establishing my students’ ability and willingness to write their reasoning, to get them to focus on communication rather than on getting a correct numerical answer. Once it’s clear that they are not taking a math course—once they see that the solution to a problem looks much more like what they’ve done in biology or economics than in calculus—I think the students will be able to move along quickly and enthusiastically through the material.

Students must get comfortable with calculation. However—as was correctly pointed out to me at the AP consultant meeting in April—if we start the course with lots of pure calculation, students will think that getting the answer is the holy grail of physics problems. If instead we begin the course demanding description, explanation, and all sorts of prose, students may become accepting of the idea that a numerical answer is merely the result of careful reasoning.

If this change in AP Physics actually works (something I’m always skeptical about in any curriculum reform, particularly at the high school level), it may help engineering students in college. Engineers do far more writing than most professions, with far less training at doing it.

I don’t think that a prompt that just says “In a clear, coherent, paragraph-length explanation, describe how you would figure out …” is going to do the trick, though. If they could already write clear, coherent paragraphs about how they would figure something out, then they would not need the curriculum change—they might not even need a physics class at the level of Physics 1.

I’m struggling with this problem in my applied circuits course, in which I require weekly design reports for the circuits they design and build. The students are staying in lab until they finish the designs and demo them, so they are clearly capable of doing the work (though not always as quickly as they should). But only a few students can explain their computations for the design parameters (like gain, corner frequency, and component values) clearly—others put down any nonsense that has a few of the right buzzwords in it.

The top students have gotten better at their explanations as a result of feedback, but the bottom students are still often producing word salad. Although there is some indication of a general writing problem (lack of topic sentences, poor grammar, and misused vocabulary), the problem is most pronounced when they are trying to explain how they selected component values. The more steps that there are in the underlying math, the more jumbled their explanations, even if the problem is just a chain of multiplications.

From time to time, I’ve suspected that the students don’t produce coherent sentences about how they computed something may not have actually done the computation, but “borrowed” the result.  This is not an explanation I believe in strongly, though, as the students have been (mostly) coming up with different solutions to the design tasks, so there isn’t simple copying going on. I’ve also seen the design process the students use, as they have been doing their pre-lab work in lab (instead of at home), so I hear them discussing the problems.  They do ask each other not just what answer they got, but how to get the answers, so they are trying to learn the method.

In looking at the pre-lab homeworks that were turned in on Monday I realized what part of the problem is—the students keep absolutely awful design notes. What the students turned in on Monday (even the top students) was mostly incomprehensible scribbling of numbers, with no indication where the numbers come from or what they were attempting to compute.  Half an hour after writing down the notes, I’m pretty sure that they could not reconstruct their reasoning—hence the often magical methods in their design reports, where they copy numbers out of their notes (some of which are correct), but can’t put together a coherent chain of reasoning that leads to those numbers. On the long multi-step computations needed to figure out what gain an amplifier needs, they can usually do each step (though often needing coaching on one or two of the steps, either by me or by one of the better students in the course), but they don’t record the meaning of each step or even what the sequence of steps is, and the “answer-getting” mentality causes them to flush the process from their minds as soon as they have a number.

I’ve seen a lot of lab exercises for other courses that try to scaffold the process by providing worksheets that give the step-by-step process and have the students fill it out as they go along. I don’t think that this is helpful though, as it encourages students to solve one step at a time and then forget about it—the scaffold prevents the students from exercising the very skill that I most need them to learn. Showing them worked examples, as I have done in class, doesn’t seem to help much either—they can follow along as I break the problem down with them, and think they understand, but then not be able to do the same thing themselves.  Again, the scaffolding prevents them from exercising the skill I most need them to learn—identifying problems and them into subproblems.

For next year, I’m probably going to have to come up with some exercises which get students to organize their thoughts external to their heads. So far, the only thing I’ve thought of is to have them create a fill-in-the-blank worksheet for each lab (like an income tax form), and turn in the blank worksheet and try filling out each other’s worksheets.  If they get in the habit of writing down the steps as steps, it may help them be able to reconstruct their work when they convert it into full sentences for the final reports. It may be too late for me to do anything formal this year (only 2.5 weeks left), but I’ll suggest it to the students anyway.

The advice I’d give to Greg Jacobs is to leave the “clear, coherent paragraph” until later in the quarter—get them to create worksheets first.

I’d welcome any suggestions from my blog readers on ways that I can get students to learn to organize their thoughts in a way that they can present them coherently to others. Block diagrams alone don’t seem to be enough, and vague things like “mind maps” are likely to do more harm than good.

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