ArduinoMania

It turns out that I won’t be teaching an introduction to programming for biologists, as I announced in February.  Funding was found for that class to be taught by the instructor who has been teaching it, freeing me up to take on a different class as overload.  (I already pretty much committed myself to teaching an overload this year.)

I decided that the most pressing need was for an applied electronic circuits course for our bioengineering majors (the current EE circuits class is way too theoretical).  The School of Engineering’s best EE instructor (Steve P.) and I had discussed doing such a course before I went on sabbatical, and our respective department chairs were enthusiastic, but funding was not found for it.  Everyone was even more enthusiastic this time around, so Steve and I are going to design the course this summer and try teaching it together in Winter (at least, if all the enthusiasm converts into a secure position for him—otherwise he’s going to have to pick up another couple of courses from a different department and not teach the new one).  We probably won’t know for sure about the funding until November, so we’re going to go ahead and design the course on spec, hoping that we get to teach it.

If Steve becomes unavailable, I don’t think I have the confidence to teach circuits by myself, since I’ve never taken a circuits course, being almost entirely self taught (my Dad taught me a little, including a German joke about a Wien bridge, when I was in high school).  After we co-teach it once, I think either of us could do the course alone, though co-teaching with a master teacher like Steve is fun.  (If the applied circuits course falls through for this year, I’ll probably try to cobble together a graduate genome assembly and annotation course, based in part on the Banana Slug Genomics class but adding a bunch of new material, so I’ll end up with a teaching overload and working on a new course this year no matter what happens.)

I’m looking forward to designing a course with Steve. We’ve both designed many courses before, and co-taught senior design project courses, but we’ve not designed a course together before. I’ve lost track of how many I’ve designed—something like 15–20, depending how you count the courses that someone else started but I extensively modified.

The approach that Steve and I are taking to the course design is to start by looking for lab projects for the students to do.  We need 10 labs (one a week for 10 weeks) ranging from very basic getting-to-know-the-equipment labs up to real (but small) design challenges.  We will try out the labs ourselves separately, then compare notes on how things went before writing up the lab handouts.  After we have the labs figured out, we’ll make sure that we cover the theory needed to understand the labs and do the designs, pacing the lectures to stay just a little ahead of the labs.  At least, that is how we both envision the process currently.

Here are a few labs that I’ve been thinking about—I’d appreciate a lot more suggestions.

• Skin conductance meter.  There are a lot of do-it-yourself lie detector circuits for measuring skin resistance (“electrodermal response” if you want to sound medical).  I like the “Lego” sensor that just uses the inputs of a Lego RCX brick to read the resistance between two fingers. But getting RCX bricks for the lab just to measure resistance is silly.
  I wonder if we should give them something that reads and records voltage (like an Arduino or other microprocessor with an A/D converter) and have them make a voltage divider to read resistance.  This could be a good first lab, with them making a single measurement with a multimeter, choosing an appropriate resistor for the voltage divider, then recording a few minutes of skin resistance, perhaps on the inside of the wrist.  We could have them use fancy silver chloride gel electrodes at 500/$80, rather than Al foil and velcro—it’d probably end up cheaper.
• When I told my son that we wanted to design the labs so that they could be done by the students without hand holding, he suggested the experiment where you pass a (small) current through a chain of people holding hands.  This might not be a bad idea also for a lecture demo.
• Electrical field measurements in an electrophoresis gel.  The students would cast a gel (possibly agarose, but maybe just agar, to make it cheaper) with a standard buffer, apply a small voltage (much less than usually used in electrophoresis, since we’ll be working without the safety shield of a closed electrophoresis box), then use a handheld voltmeter to measure the voltage at different points in the gel.  We would also have them measure voltage and current.  We might even have them time the movement of a loading dye at different voltages, but I think that would take too long.
  One problem with this lab is that it requires using the wet lab, and neither Steve nor I are really wet-lab people.  I wonder if we could borrow a TA for a week from another course.  Perhaps a bioengineering senior undergrad could be hired, as many of them have some experience at casting gels.
• Conductivity of saline solutions.  It is standard to measure the ionic content of fresh water and even sea water by measuring its conductivity—Wikipedia has a decent article on the theory of electrolyte conductivity.  A conductivity calculator gives an equivalence of 1 ppm total dissolved solids as 1.56 µS/cm, though they don’t specify the temperature or include a temperature correction.  The City of Santa Cruz 2011 Consumer Confidence Report lists the drinking water in town as 280–760 µS/cm (though they use the charming older name: µmhos/cm), while a 2004 San Lorenzo River Watershed Management Plan gives the conductivity in the estuary as 260–44,860 µS/cm, depending when and where the sample is taken (though they label their table wrong)
  The tricky part here is that the conductivity testing has to be done with an AC signal, not a DC one, to avoid problems at the electrodes. If we trust the students not to spill salt water into the equipment, we could probably do this lab in the electronics lab, and use the bench oscillator and meters.  Later in the quarter we might have them design their own rectifier circuit to communicate with a microprocessor, but I suspect that doing an oscillator may be beyond the scope of the class.
  We may also want to get silver/silver chloride electrodes (or fine silver wire at $0.90/foot and soak it in bleach).    Using thin wires as the electrodes may cause problems with the resistance being very high.  I wonder if we should try doing something cheaper first, like using a pair of pennies cleaned in vinegar and rinsed.  They wouldn’t last long in salt water, but even demonstrating the problem might be instructive.
• A good project for late in the quarter would be a do-it-yourself EKG, which requires a simple amplifier (and gets another use for the silver/silver-chloride gel electrodes).
• We could also do an optical pulse detector, using an LED and a light sensor, though we’d probably end up making our own, rather than buying one for $20.
• Breathalyzer.  A resistance-output sensor for alcohol on the breath looks like it only costs about $5.  This may be too simple.
• [Added 14 June 2012, after first publishing this post] Thermistors. A different application of voltage dividers, and one that would be relevant for both EE and BIOE students is thermistors.  The intro at http://www.mstarlabs.com/sensors/thermistor-calibration.htmlgives a nice overview of the subject for students. This would be a cheaper lab than the gel electrophoresis, with less cleanup needed.It would be easy to do three temperatures in water baths (ice water, room temperature water, hot water) and do 3-point calibration.  The design exercise of figuring out the best resistance to get fairly linear voltage vs. temperature plot is a useful one, and not too hard (I think).

Several of these labs look like they would be most interesting if they involved hooking up to an Arduino or other cheap microprocessor that can record time-course data.  Since programming is outside the scope of the circuits course, we could have the students buy an Arduino for about $20–30 online and give them a simple recording program (perhaps I can get my son to write them a versatile one, based on the one he wrote for our super pulley recording).  The students could sell the Arduino used if they weren’t interested in doing anything with it (the Digital Arts and New Media students use them and probably would be glad of cheap ones).

Obviously, we’re going to need more lab ideas.  Does anyone have any?

It turns out that I won’t be teaching an introduction to programming for biologists, as I announced in February.  Funding was found for that class to be taught by the instructor who has been teaching it, freeing me up to take on a different class as overload.  (I already pretty much committed myself to teaching an overload this year.)

I decided that the most pressing need was for an applied electronic circuits course for our bioengineering majors (the current EE circuits class is way too theoretical).  The School of Engineering’s best EE instructor (Steve P.) and I had discussed doing such a course before I went on sabbatical, and our respective department chairs were enthusiastic, but funding was not found for it.  Everyone was even more enthusiastic this time around, so Steve and I are going to design the course this summer and try teaching it together in Winter (at least, if all the enthusiasm converts into a secure position for him—otherwise he’s going to have to pick up another couple of courses from a different department and not teach the new one).  We probably won’t know for sure about the funding until November, so we’re going to go ahead and design the course on spec, hoping that we get to teach it.

If Steve becomes unavailable, I don’t think I have the confidence to teach circuits by myself, since I’ve never taken a circuits course, being almost entirely self taught (my Dad taught me a little, including a German joke about a Wien bridge, when I was in high school).  After we co-teach it once, I think either of us could do the course alone, though co-teaching with a master teacher like Steve is fun.  (If the applied circuits course falls through for this year, I’ll probably try to cobble together a graduate genome assembly and annotation course, based in part on the Banana Slug Genomics class but adding a bunch of new material, so I’ll end up with a teaching overload and working on a new course this year no matter what happens.)

I’m looking forward to designing a course with Steve. We’ve both designed many courses before, and co-taught senior design project courses, but we’ve not designed a course together before. I’ve lost track of how many I’ve designed—something like 15–20, depending how you count the courses that someone else started but I extensively modified.

The approach that Steve and I are taking to the course design is to start by looking for lab projects for the students to do.  We need 10 labs (one a week for 10 weeks) ranging from very basic getting-to-know-the-equipment labs up to real (but small) design challenges.  We will try out the labs ourselves separately, then compare notes on how things went before writing up the lab handouts.  After we have the labs figured out, we’ll make sure that we cover the theory needed to understand the labs and do the designs, pacing the lectures to stay just a little ahead of the labs.  At least, that is how we both envision the process currently.

Here are a few labs that I’ve been thinking about—I’d appreciate a lot more suggestions.

• Skin conductance meter.  There are a lot of do-it-yourself lie detector circuits for measuring skin resistance (“electrodermal response” if you want to sound medical).  I like the “Lego” sensor that just uses the inputs of a Lego RCX brick to read the resistance between two fingers. But getting RCX bricks for the lab just to measure resistance is silly.
  I wonder if we should give them something that reads and records voltage (like an Arduino or other microprocessor with an A/D converter) and have them make a voltage divider to read resistance.  This could be a good first lab, with them making a single measurement with a multimeter, choosing an appropriate resistor for the voltage divider, then recording a few minutes of skin resistance, perhaps on the inside of the wrist.  We could have them use fancy silver chloride gel electrodes at 500/$80, rather than Al foil and velcro—it’d probably end up cheaper.
• When I told my son that we wanted to design the labs so that they could be done by the students without hand holding, he suggested the experiment where you pass a (small) current through a chain of people holding hands.  This might not be a bad idea also for a lecture demo.
• Electrical field measurements in an electrophoresis gel.  The students would cast a gel (possibly agarose, but maybe just agar, to make it cheaper) with a standard buffer, apply a small voltage (much less than usually used in electrophoresis, since we’ll be working without the safety shield of a closed electrophoresis box), then use a handheld voltmeter to measure the voltage at different points in the gel.  We would also have them measure voltage and current.  We might even have them time the movement of a loading dye at different voltages, but I think that would take too long.
  One problem with this lab is that it requires using the wet lab, and neither Steve nor I are really wet-lab people.  I wonder if we could borrow a TA for a week from another course.  Perhaps a bioengineering senior undergrad could be hired, as many of them have some experience at casting gels.
• Conductivity of saline solutions.  It is standard to measure the ionic content of fresh water and even sea water by measuring its conductivity—Wikipedia has a decent article on the theory of electrolyte conductivity.  A conductivity calculator gives an equivalence of 1 ppm total dissolved solids as 1.56 µS/cm, though they don’t specify the temperature or include a temperature correction.  The City of Santa Cruz 2011 Consumer Confidence Report lists the drinking water in town as 280–760 µS/cm (though they use the charming older name: µmhos/cm), while a 2004 San Lorenzo River Watershed Management Plan gives the conductivity in the estuary as 260–44,860 µS/cm, depending when and where the sample is taken (though they label their table wrong)
  The tricky part here is that the conductivity testing has to be done with an AC signal, not a DC one, to avoid problems at the electrodes. If we trust the students not to spill salt water into the equipment, we could probably do this lab in the electronics lab, and use the bench oscillator and meters.  Later in the quarter we might have them design their own rectifier circuit to communicate with a microprocessor, but I suspect that doing an oscillator may be beyond the scope of the class.
  We may also want to get silver/silver chloride electrodes (or fine silver wire at $0.90/foot and soak it in bleach).    Using thin wires as the electrodes may cause problems with the resistance being very high.  I wonder if we should try doing something cheaper first, like using a pair of pennies cleaned in vinegar and rinsed.  They wouldn’t last long in salt water, but even demonstrating the problem might be instructive.
• A good project for late in the quarter would be a do-it-yourself EKG, which requires a simple amplifier (and gets another use for the silver/silver-chloride gel electrodes).
• We could also do an optical pulse detector, using an LED and a light sensor, though we’d probably end up making our own, rather than buying one for $20.
• Breathalyzer.  A resistance-output sensor for alcohol on the breath looks like it only costs about $5.  This may be too simple.

Several of these labs look like they would be most interesting if they involved hooking up to an Arduino or other cheap microprocessor that can record time-course data.  Since programming is outside the scope of the circuits course, we could have the students buy an Arduino for about $20–30 online and give them a simple recording program (perhaps I can get my son to write them a versatile one, based on the one he wrote for our super pulley recording).  The students could sell the Arduino used if they weren’t interested in doing anything with it (the Digital Arts and New Media students use them and probably would be glad of cheap ones).

Obviously, we’re going to need more lab ideas.  Does anyone have any?