(Last Update: 2016 March 18 16:14 PDT )
This freshman design seminar is a limited to first-year students (second-year allowed in if there is room) who are proposed bioengineering majors. Class size is limited due to limited lab capacity.
This is a first course in engineering design for bioengineers. Students choose a design project and work on it in cooperative teams. Covers team building, design, prototyping, and report writing.
The current goal for the design projects is to have small teams (2–3 students) design low-cost lab equipment suitable for hobbyists or home school, middle school, or high school science labs. Think of it as "science on a shoestring" or "thrift-store science". We'll be trying to duplicate the functionality of expensive science teaching tools (such as those sold by Pasco and Vernier) at a fraction of the price. But the course is driven by what the students want to learn and do—if you have an idea for a project, bring it up in class.
A major goal of the course is to get students thinking like engineers: asking questions like "How can we make something that does this?", "What are the constraints on the design?", "Will this part do what we want?", "How much would it cost to do that?"
Another goal of the class is to get students to learn on their own to meet their own needs for knowledge, rather than relying on teachers to tell them what to learn. Initially, you'll be directed to look for certain information, to develop your skills at finding and evaluating information—later you'll be asking your own questions that need answers.
Take this course because you want to do it, not because you have to. Because it does not satisfy any BSoE major requirements, it is reasonable to take the course P/NP, instead of for a grade. Expect to average about 6 hours/week on the course, perhaps a bit more if your group gets excited about their project.
Please feel free to leave comments on the blog with suggestions for the course.
If you qualify for classroom accommodations because of a disability, please submit your Accommodation Authorization from the Disability Resource Center (DRC) to me during my office hours in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY).
Anyone caught cheating in the class will be reported to their college provost (see UCSC policy on academic integrity) and may fail the class. Cheating includes any attempt to claim someone else's work as your own. Plagiarism in any form (including close paraphrasing) will be considered cheating. Use of any source without proper citation will be considered cheating. If you are not certain about citation standards, please ask, as I hate having to fail students because they were improperly taught how to cite sources.
Collaboration without explicit written acknowledgment will be considered cheating. Collaboration on all assignments with explicit written acknowledgment is encouraged—guidelines for the extent of reasonable collaboration will be given in class.
I'll want to see the logs weekly, so that I can adjust assignments to avoid overworking students. Perhaps the simplest thing to do is to keep the log as a Google spreadsheet and give me (karplus@soe.ucsc.edu) read access to the spreadsheet—make sure the spreadsheet has your name on it, so I can keep them straight, as Google provides only non-mnemonic names for files.
We'll look at different student spreadsheet designs in class, to take good ideas from each other.
Your next assignment is to pick projects from two other students and research them further, looking for more information, other design choices for the same result, possible problems with doing the design, workarounds for the problems, and so forth.
For each project you research, you should send an email to the class mailing list (bme88a-w16@soe.ucsc.edu), sharing what you have found and thought about. Discuss only one project in each email, and use BME88A and the project name (PCR machine, UV sensor, photogate, incubator, pulse monitor, ...) as the subject line of the message, so that others can find the messages about particular projects more easily. Respond to each other's research—if some one has identified a possible problem, and you've got an idea how to solve that problem or have found a resource on the web that addresses it, reply to everyone to contribute to the discussion!
I am expecting at least two email messages (two different projects) on the email list from each of you—sooner is better, so that everyone can read and think about your ideas before Monday's class. I hope that we can then discuss the projects that students found most interesting in class, with several people having already looked at the projects in some detail.
I want you to design a colorimeter for measuring OD600 in the cuvettes you got. (Keyword=optical density) (also look up what OD600 is used for in monitoring cultures)
Design the mechanical part of the colorimeter so that the light source and photosensor are on opposite sides of the cuvette in a straight line perpendicular to the faces of the cuvette and there is no ambient light on the photosensor.
You might want to get yourself a razor knife (Exacto knife or cheaper equivalent) for cutting and scoring foam core (I have a few, but not enough to provide one for everyone).
I want each pair to build a prototype colorimeter that can measure the light coming through a cuvette. Your design needs to
Optional bonus assignment (programming): have the program record the
light through a cuvette filled with water, and use that as reference
to compute absorbance:
log_10 ( light with just water / light with absorbing material)
For sizing the resistor on the phototransistor, you'll need to know how much current to expect—see https://gasstationwithoutpumps.wordpress.com/2016/01/26/phototransistor-i-vs-v-plots/ for a plot of the current vs. voltage that I measured for the phototransistor, illuminated by one of the LEDs.
Be prepared on Friday 2016 Jan 29 to ask for the resistor(s) you need for your design.
Also, by that date you should have ordered all the parts you need.
Some of the software needs to be written—include it as an appendix to the report.
In this draft of the final report, indicate any changes to the design, progress on building the prototype, difficulties you need help resolving, and so forth.
The homework listed below here is based on the Winter 2015 offering of the course. I expect the homework to be different this year, as what students need to learn will depend on what the students in the class want to pursue as projects. The web page will be updated as the class progresses.
Note: due dates below here are probably too late for completion of projects. We'll try to get projects started earlier this year.
The following circuit may not be identically labeled to the one I showed in class. I've also used batteries and a voltmeter here to make it clearer exactly what voltages we are talking about.
Here is the circuit I gave in class. The labeling may be different from what I drew on the board, since this is an old version of the schematic that I happened to have in Scheme-It:
The schedule listed here is based on the Winter 2015 offering of the course, to give a rough idea of how the class might go. The web page will be updated as the class progresses.
Date | Lecture Topic(s) | Due |
---|---|---|
Mon 2016 Jan 4 | administrivia, discussion of time log, need for group projects | intake survey |
Wed 2016 Jan 6 | Design review of time-log spreadsheets, passed around some microcontroller boards and discussed choice of boards. We settled on Teensy LC or Teensy 3.2 | |
Fri 2016 Jan 8 | Availability of styrofoam boxes for inclubators. Collected orders for microcontroller boards. Basic notion of colorimeters, passed out Brand 759076D cuvettes. Discussed foamcore as prototyping material. Ohm's Law. | ideas for interesting projects |
Mon 2016 Jan 11 | what is a diode? How does it work? anode and cathode (cathode where electrons leave the wire—works for vacuum tubes, chemical reactions, and semiconductors). Depletion region, I vs. V curve, How does an LED work? Lumens as 683.002 integral power(lambda) luminosity(lambda) d lambda. Candela as lumen/steradian (and definition of steradian). Illuminance in lumens/m^2 (or W/m^2). | read about colorimeter and spectrometer |
Wed 2016 Jan 13 | LED data sheet, I-vs-V curve, current-limiting resistors. Spectrum for LED, peak vs. dominant wavelength, spectrum for lighting LEDs, bandwidth (45nm for LED, 5nm for laser diode). | |
Fri 2016 Jan 15 | sold Teensy boards and breadboards at cost. Worked example of blinky-light program on Teensy using Arduino interface. (both on-board pin 13 and LED with current-limiting resistor on pin 10) | |
Mon 2016 Jan 18 | MLK Day, no class | |
Wed 2016 Jan 20 | Day in electronics lab (Baskin 150). Soldering headers onto Teensy boards. multimeters, power supplies, hand out 600nm LEDs (student choice of LTL-4273 and 333-2UYC/H3/S400-A6), phototransistors (LTR-4206), and foamcore. | |
Fri 2016 Jan 22 | phototransistors | |
Mon 2016 Jan 25 | Baskin 150: finish soldering, start wiring colorimeters. Hand out foam core. | |
Wed 2016 Jan 27 | Discussion of popular project possibilities: selection of top 3. Ended up with ultrasonic rangefinder, LED cube with capacitive touch keyboard, and optical pulse monitor. Intro to using PteroDAQ for debugging colorimeter hardware. | |
Fri 2016 Jan 29 | Discussed design parts (electronic, programming, mechanical) for colorimeter. Partnerwork styles (alternating work/critique, division of labor, independent design and compare). I-vs-V for phototransistor, sizing resistors for colorimeter, Worked example of colorimeter code (no demo). analogReadRes(16), analogReadAveraging(32), touchRead(A9). Reminder to complete lab safety training. Brief discussion of theory of ultrasonic rangefinder. Announced expected delivery Feb 5–Feb 24 of TCT40-16R/T 40KHZ transducers. | |
Mon 2016 Feb 1 | Debugging colorimeter prototypes. | Colorimeter prototypes |
Wed 2016 Feb 3 | Finish colorimeter prototypes. Components of a design report, including design goals (specifications), block diagrams, schematics, mechanical drawings, photos, and explanations for all design choices. Gain/sensitivity/efficiency. Intro to amplifiers. | |
Fri 2016 Feb 5 | Announcements: register for lab safety training (BELS didn't enter students as they said they would), update time logs, design reports are due Monday, PteroDAQ is broken on OS X 10.11 (will try to fix this weekend). Suggestions for groups: LED cube groups: try making touch sensors and reading them with touchRead(), trying both simple plates and interdigitated gnd and pin, work out how to do 3D soldering; Pulse monitor group: figure out physical mounting (through finger, through earlobe, reflection sensor?) and choose wavelength; Ultrasonic rangefinder group: transceivers arrived, outline what needs to be done for both hardware and software. Rest of lecture: ideal op amps, negative feedback amplifier, non-inverting amplifier, unity-gain buffer, inverting amplifier. Gain-bandwidth product. | |
Mon 2016 Feb 8 | op amp review, transimpedance amplifier, multistage amplifier, high-pass RC filter, LED grid for reducing pins by time multiplexing, Charlieplexing, 1-of-n decoder. | Colorimeter design report |
Wed 2016 Feb 10 | amplifiers with single power supply. | |
Fri 2016 Feb 12 | Oscilloscopes in EE lab | |
Mon 2016 Feb 15 | Presidents' Day, no class | |
Wed 2016 Feb 17 | Feedback on colorimeter design reports. Hysteresis oscillator in touchRead() for Teensy. | |
Fri 2016 Feb 19 | Time multiplexing for LED cube (192 LEDs with 16 output pins, using 16-fold time multiplexing), 4-to-16 demux, current-limiting resistors, nFETs, pFETs, threshold voltage, adding 5V inverter to get easier threshold voltage specs on pFET. | |
Mon 2016 Feb 22 | How optical pulse monitor works (systolic/diastolic pressure, restricted flow). Demo of pulse monitor—with PteroDAQ, with digital filter to remove baseline drift reporting waveform, with pulse caller and mean or median filtering. RC low-pass and high-pass filters. Intro to digital signal processing: discrete values, discrete time, sampling frequency, mention of bessel filters as best design choice for time-domain analysis. | Design specs for project |
Wed 2016 Feb 24 |
Review (requested by students) of Vgs computation for nFET and pFET in LED multiplexing. Digital filters: z-transform, transfer function, handwaving H(e^(jw)) as response to sinusoid e^(jwt), FIR block diagram and pseudocode, IIR (biquad) block diagram and pseudocode with derivation of transfer function. Plotted gain functions for biquad filter for pulse monitor and for all-zero bandpass (1-z^-2). Biquad plotting code in biquad.gnuplot. Showed python code for selecting biquad filter parameters: design-bandpass.py. Mentioned in e-mail, but only alluded to in class: I was looking for a good introduction to digital filters to provide backup for the lectures this week. So far, the best I've found is https://ccrma.stanford.edu/~jos/filters/ which is aimed at musicians doing computer music, so starts out at a fairly low level. The organization as a html document with many tiny pages makes reading it a bit tedious, though. http://www.dspguide.com/ch14.htm initially looked promising, but it doesn't get to the meat of the material until the end of the book, which makes it a lot of reading for relatively little directly useful content. The application note http://www.intersil.com/content/dam/Intersil/documents/an96/an9603.pdf has some good intro, but is aimed mainly at engineers, so gets rather technical quickly. Not covered: a Python bandpass filter program for filter PteroDAQ output files, in EKG_demo. | |
Fri 2016 Feb 26 |
Choosing capacitors for RC filters, breaking bandpass into
separate low-pass and high-pass with an amplifier, standard
values for resistors (E24 series) and capacitors (E6 series)
(see http://www.logwell.com/tech/components/resistor_values.html).
Unpacking binary numbers into digitalWrite() commands to output multi-bit numbers (for the LED cube projects). | |
Mon 2016 Feb 29 | Timing (busy wait, delay loop, IntervalTimer to set up interrupt) Example code in wait_micros, delay_loop, and interval_timer. | More detailed design report draft |
Wed 2016 Mar 2 | Meet in Baskin 150 for lab time | |
Fri 2016 Mar 4 | Meet in Baskin 150 for lab time | |
Mon 2016 Mar 7 | Meet in lab Baskin 150 | Progress report |
Wed 2016 Mar 9 | Meet in lab Baskin 150 | |
Fri 2016 Mar 11 | Meet in lab Baskin 150 | |
Tues 2016 Mar 15 4–7 | final exam slot, Baskin 150 | all reports and demos |
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