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2014 November 17

Faculty writing community

Filed under: Circuits course — gasstationwithoutpumps @ 20:35
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Eric L. Muller wrote in Developing the Faculty as a Writing Community | AAUP,

I have also come to see how many other pleasures and labors of life are enhanced by companionship and accountability. Lots of people exercise more in groups, read more books with groups, lose more weight in groups. Wouldn’t it stand to reason that many faculty members might write more in groups, too?

That was a question that the Center for Faculty Excellence (CFE) at UNC at Chapel Hill set out to explore in the summer of 2013. The CFE is the university’s pan-campus faculty development center. Together with the Institute for the Arts and Humanities in the College of Arts and Sciences, the CFE piloted the Summer Writing Group program for faculty members across the university. The response was enthusiastic.

He went on to describe what sounds like a fairly successful experiment in faculty development.  I note that it did not appear to include any engineering or science faculty, though perhaps there were one or two in the “completely interdisciplinary” groups.

It sounds like an interesting idea, and it probably would have helped me last summer while I was trying to work on my textbook for the bioengineering electronics class.  I ended up practicing all sorts of “creative procrastination” instead of writing.  I got some stuff done on the book over the summer, but not nearly as much as I had hoped at the beginning of the summer. A writing group may have helped me keep my nose to the grindstone (a metaphor I’ve always found rather gross if taken literally).  I don’t know how much I’ll get done before I have to use the book in the Spring, since I’m teaching two classes each quarter, as well as all the work of being undergrad director and program chair for the bioengineering program.

I’ve not been part of writing group since grad school, when I was in a poetry-writing group with a bunch of people twice my age or older. Having a monthly meeting did help me then, and it was important that we read each others’ work and took it seriously (not just providing rah-rah comments). I’m not sure that the UNC approach would help much, unless the other faculty were close enough in their expertise to be willing and able to read and comment on the draft chapters.

Have any of the faculty who read this blog ever participated in anything like the UNC summer writing group? Did it help you keep to a schedule? Was it important to share drafts with each other?


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.

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