UCSC BME 88A Winter 2015

Overview

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 competitive and cooperative teams. Covers team building, design, prototyping, and report writing.

Instructor:

Kevin Karplus karplus@soe.ucsc.edu

Office hours:

PSB 318, M 3–4, Th 3–4

Meeting times:

MWF 12:30–1:40, Physical Science Building 305
We'll sometimes meet in the EE circuits lab (Baskin Engineering 150), or the fabrication lab (Baskin Engineering

Group Tutor:

None hired yet

E-mail discussion

There is an e-mail discussion group for the class. All students in the class should participate in e-mail discussions. Other people may request joining the discussion, to be allowed in or not at the discretion of the class.

Overview:

This course is new 2-unit freshman design seminar, a concept suggested by BMES, the student BioMedical Engineering Society. The course was offered as a prototype in Winter 2014 (as BME 94F) and is still under active development. Students will be helping design the course, as well whatever design projects we take on.

The current goal for the design projects is to have small teams (2–4 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.

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.

Target audience:

The primary audience are freshman bioengineering majors and premajors. If space permits, we may allow in a few 2nd-year or transfer students. Seniors interested in the course are encouraged to attend the first day and apply to be group tutors.

Prerequisites:

This is intended for first-year students, so there are no prerequisites. Students should come in with an interest in designing and constructing things. Prior experience with hand tools, soldering, computer programming, and so forth are all valuable, but no specific skills are required to join the class.

Requirements satisfied:

This course does not satisfy any bioengineering graduation requirements, nor is it a prerequisite for any further courses. It does provide a PR-E (Collaborative endeavor) general-education code.

Take this course because you want to do it, not because you have to. Expect to average about 6 hours/week on the course, perhaps a bit more if your group gets excited about their project.

Evaluation:

Students will be evaluated on the written, oral, or poster presentations of their designs, as well as on how well their prototypes meet the design goals they set.

Homework

Intake survey Do in class Mon, 2015 Jan 5.
Turn in by e-mail by midnight Friday, 2015 Jan 9: Look on-line for projects that might be interesting to design or build this quarter. Look at sites like Pasco, Vernier, and Arbor Scientific for ideas about what schools with money have in their labs. Look for do-it-yourself lab equipment ideas on the web. Turn in an annotated list of URLs for interesting sites as plain text, cut-and-pasted into e-mail to karplus@soe.ucsc.edu. Even better, mail to the whole class at bme88a-w2015@soe.ucsc.edu. The annotation need not be extensive—a sentence about each web site, telling us what project(s) it has information about, should suffice. Raw URLs without annotation, however, are not acceptable. You should also explore whether the full URL is needed to get to the site—a lot of web sites add all sorts of extra tracking or status junk to URLs, and it is good practice to strip the URLs down to the essentials.
Before 2015 Jan 12, look up how a spectroscope, spectrophotometer, spectrometer, and colorimeter works. Try to find some DIY versions. (Note: there are two different instruments called "colorimeter"—the one I mean is the the one used in chem labs for measuring the absorbance of light by a chemical solution, not the one used for determining the color of light emitted by a monitor or reflected from an object.)
Question: is a photospectrometer a good design task? Should we start with a colorimeter? We should get some lab time to build some of the designs!
DUE Friday, 2015 Jan 16. I have constructed a list of all the student-suggested projects at https://gasstationwithoutpumps.wordpress.com/2015/01/10/student-project-ideas-for-freshman-design-seminar/
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-w2015@soe.ucsc.edu), sharing what you have found and thought about. Discuss only one project in each email, and use the project name (PCR machine, UV sensor, photogate, ...) 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 by class time on Friday 16 Jan—sooner is better, so that everyone can read your ideas before Friday's class. I hope that we can then discuss the projects that students found most interesting in class on Friday, with several people having already looked at the projects in some detail.
I am buying some LEDs, photodiodes, and phototransistors for your use.
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)

The LEDs I'm buying are WP710A10ND

You'll have a choice of two photosensors: photodiode PD204-6C or phototransistor SFH 310-2/3. Look up the specs for these parts (Digi-key has them) and try to figure out how you would wire them up to light up the LED (without exceeding its maximum current) and sense the light with the photosensor.

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.

I'll also try to buy some black foam core, so that you'll be able to build your designs. 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).

We should have the parts in time for class Friday 30 Jan 2015, so bring your breadboards, redboards, schematics, drawings, and so forth to class then.
Turn in Wed 2015 Feb 18: Design report for a colorimeter. A design report starts with a clear specification of the design goals: what does the device do? what constraints (cost, size, power avaiable, and so forth) are there? The report continues with how you met the design goals, what problems arose, and how the problems were solved. There should be schematics for all electonics, complete with component values. There should be explanations (often computations) for how component values were chosen. There should be drawings, photographs, or both, sufficient for someone else to duplicate the physical design. Any external sources used should be clearly cited. As with all engineering documents, the authors' names and the date of the last revision should be on the first page, and all pages should be numbered. If you have any questions, please e-mail the bme88a-w2015@soe.ucsc.edu mailing list, so that I can respond where everyone can read the answer.
By Fri 2015 Feb 20, give me the names of each group of 2 or 3 students and what project you are working on. In class, we narrowed the list down to three projects:
- Blood Pressure Monitor: 8 expressed interest, so currently need to form 3 groups.
- Optical Heart Rate Monitor: 3 expressed interest, so currently one group.
- EKG/EMG: 3 expressed interest, so currently one group
The data files and filter program for the EKG demo on Wed Feb 18 and Fri Feb 20 are available at EKG_demo.
Turn in Wed 2015 Feb 25: Design proposal (one per group), containing at least:
- Design specifications: what exactly are you designing? what does it do? How can I tell whether or not you've designed what you intended?
- Block diagram: what are the subsystems of your design? How are they connected? What are the specifications for the interfaces?
- Desing problems: what resources, parts, tools, educations, ... do you need to design and make for your block diagram to work?
This design proposal is a first draft of the final report, and you will keep adding to it for the rest of the quarter.
Turn in Fri 2015 Feb 27: Work individually and show derivations for formulas (based on Ohm's law):
1. What is output voltage of voltage divider if the two inputs are connected to V_A and V_B instead of to V_in and GND? (Given: no current through the output port.)
  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.
2. What is the formula for the output of a negative-feedback op amp circuit? (Given: no current through the inputs of the op amp, and negative feedback holds the two inputs of the op amp to the same voltage.)
  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:
By Monday 2 March 2015, order the parts you need. Turn in Monday 2 March 2015, redone design proposals.
Turn in Fri 2015 Mar 6 Changed to Mon 2015 Mar 9: a progress report that is a draft of the final report, indicating any changes to the design, progress on building the prototype, and so forth.

Schedule

Date	Lecture Topic(s)	Due
Mon 2105 Jan 5	administrivia, intro to electronics	intake survey
Wed 2105 Jan 7	what is a diode? also passed around some processor boards and handed out Brand 1.5ml (759076D) cuvettes for them to start thinking about colorimeter/spectrometer design
Fri 2105 Jan 9		ideas for interesting projects
Mon 2105 Jan 12	difference between colorimeter and spectrometer, light sources for colorimeter (LED), spectrum for LED, peak vs. dominant wavelength, spectrum for lighting LEDs, bandwidth (45nm for LED, 5nm for laser diode), monochromator, ordered Sparkfun redboards and breadboards.	read about colorimeter and spectrometer
Wed 2105 Jan 14	lab tours (protein engineering and nanopore labs)
Fri 2105 Jan 16	laser pointers and diffraction grating demo (also using bike head lamp), somewhat incorrect mention of Bragg's Law (no formula)—I should have pointed to the Wikipedia article Diffraction grating instead, design practice to come up with need to rotate the light source and grating relative to the sample and light detector.
Mon 2105 Jan 19	MLK Day, no class
Wed 2105 Jan 21	sold redboards and breadboards at cost. Discussion of popular project possibilities.
Fri 2105 Jan 23	photodiodes
Mon 2105 Jan 26	LEDs
Wed 2105 Jan 28	phototransistors
Fri 2105 Jan 30	day in the electronics lab, multimeters, power supplies, handed out 600nm LEDs and phototransistors or photodiodes, and foamcore.
Mon 2105 Feb 2	in electronics lab, students measured current in photodiodes or phototransistors, requested resistors, started building foamcore prototypes
Wed 2105 Feb 4	intro to blood pressure and pressure sensor demo (used Arduino, not KL25Z)
Fri 2105 Feb 6	more lab time on colorimeter
Mon 2105 Feb 9	more lab time on colorimeter
Wed 2105 Feb 11	planned to do EKG demo, but left laptop at home.
Fri 2105 Feb 13	last colorimeter lab
Mon 2105 Feb 16	Presidents' Day, no class
Wed 2105 Feb 18	schedule remaining assignments, discuss preliminary design report (specifications, block diagram, design/resource problems), EKG demo (with bandpass filter)	Colorimeter design report
Fri 2105 Feb 20	Filtering to remove baseline drift and 60Hz noise. The cleaned up bandpass-filter.py program is at EKG_demo.)	Groups and projects
Mon 2105 Feb 23	Feedback on writing, voltage dividers, amplifiers.
Wed 2105 Feb 25	RC filters. Draft of book posted on line	Preliminary design report
Fri 2105 Feb 27	Breaking design in parts, solutions to voltage divider and op amp exercises. Posted sample cuff pressure measurement, gnuplot script, and resulting plot.	Voltage divider and op-amp exercise.
Mon 2105 Mar 2	block diagrams for EKG and blood pressure monitor	order parts
Wed 2105 Mar 4	instrumentation amp use, pin numbers on schematics, data sheet for INA126P, high-pass RC filter (0.5Hz), RC time constant, data sheet for MPX5050, practice with blood pressure cuff, checking out cuffs.
Fri 2105 Mar 6	wiring V_ref, busy waiting: developed example periodic_timer.ino, some discussion of difference between interrupts and busy waiting.
Mon 2105 Mar 9	Meet in lab BE 150	Progress report
Wed 2105 Mar 11
Fri 2105 Mar 13	Meet in lab BE 150
Mon 2105 Mar 16	Meet in lab BE 150
Tues 2015 Mar 17 12–3	final exam slot	all reports and demos

SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

Questions about page content should be directed to Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
318 Physical Sciences Building

BME 88A W15
BMES Freshman Design Seminar

Overview

Blog

Homework

Schedule

BME 88A W15 BMES Freshman Design Seminar

Overview

Blog

Homework

Schedule

BME 88A W15
BMES Freshman Design Seminar