(Last Update: 2013 December 19 14:28 PST )

Overview

This offering of BME 194 is a prototype run for a new course: "Applied Circuits for Bioengineers".

The course is intended for sophomores and juniors in biomolecular engineering, but is open to anyone who meets the prerequisites:

Calculus (Math 11B, 19B, or 20B, or AP Calculus BC with 4 or 5)
Physics Electricity and Magnetism (Physics 5C or 6C, or AP Physics C: E&M with 4 or 5)

The theme for the course is "connecting real-world signals to computers using analog electronics", and we will be working with interfacing thermistors, microphones, electrodes, photo-detectors, capacitance sensors, and strain-gauge pressure sensors to Arduino microprocessors. The final lab will be the design, implementation, and testing of a small single-channel electrocardiogram (or electromyogram).

The Bioengineering major will accept this course as fulfilling the EE101/L (circuits) requirement, but EE will not be accepting it as a prerequisite for further electronics courses. It is possible to take both the Applied Circuits course and EE 101/L for credit, though there is substantial overlap in content.

To take the prototype version of the Applied Circuits course, register for both
BME 194 Section 01 class #31115 MWF 2–3:10 PSB 140 (5 units)
BME 194F Section 01 class #31118 Th 2–5 Baskin Engr 150 (2 units)

Currently, the best description of the course is on Prof. Karplus's blog:
http://gasstationwithoutpumps.wordpress.com/circuits-course-table-of-contents/
but most students probably don't want to read the hundreds of pages of notes there on the design of the course. For a shorter description that is now a little out of date, try
http://gasstationwithoutpumps.wordpress.com/2012/09/29/supplemental-sheets-draft-2/

Students will learn to use standard electronics equipment (multimeters, oscilloscopes, function generators, power supplies) and tools (pliers, wire strippers, breadboards, soldering irons). The course is an engineering design course—we aim to make the labs require design, not just cookbook procedures. The complexity of the design tasks should ramp up through the quarter.

Because this is a prototype course, we will seek frequent feedback from the students in the course about improvements that can be made. Undoubtedly some of what we currently plan will be extensively modified during the quarter.

Instructors and Assistants

• Kevin Karplus Office Physical Sciences Building 318, Mon 3:30–4:30
• Stephen Petersen, Office Baskin Engr. 251, TBA
• Ivan Tenorio-Amador (lab assistant)

What to buy

Tools and Parts

The class is limited to 20 students, as that is the number of parts kits that were assembled during winter break. Some of the parts take weeks to arrive and are expensive to buy in single quantities, so we will not be able to add people to the class later. The parts kit will cost $65.50 (the full list of parts and costs). Also, Prof. Karplus had to buy these parts out of his own pockets for resale at cost, as there was not time to set up a lab fee for the course (parts were still being add to the parts list as late as the Friday before classes started).

Parts and tools kits will be sold on Wed 2013 Jan 9, so that students will have them before the first lab on Thursday. Please bring cash or checks made out to "Kevin Karplus" to that class. We'll also spend some of class time going over what is in the kit.

Arduino

There is one item that we want students to buy on their own: an Arduino microprocessor. We've been testing the software we use with an Arduino Uno, an older Arduino Duemilanove, and (most recently) with an Arduino Leonardo as well. The Arduino Due uses a different processor and will not work. Be sure to get the right USB cable for your board (the Leonardo uses a smaller micro-B connector than the Uno). Cost should be about $21–30 plus $3–4 for the USB cable plus shipping, but it may be possible to get a used one from other students, as other courses also use this board.

The Leonardo has a faster transfer rate possible, and a bit more flexibility in which pins can be used for analog input, but for the labs we'll do, it doesn't matter much which of the boards you get.

Warning: some of the "Arduino compatible" and "Arduino Pro" boards don't include the USB connection, but you will need that.

Warning: Some of the Leonardo boards are sold without headers (for people who want to solder them directly into projects), but you will need the headers to plug wires in temporarily. You can solder on headers if you bought a board without them—you'll need one 6-long, two 8-long, and one 10-long female header for the Leonardo.

Software

All the software you need to use is installed on the lab computers, but you may want to get your own copies for use on your laptop. All the software is free:

DataLogger download
DataLogger instructions
Arduino development environment download
Python (either 2.7 or 3.3)
PySerial installation instructions
gnuplot

Data Logger code was developed specifically for this course, and is available from http://bitbucket.org/abe_k/arduino-data-logger/downloads under the "Tags" tab. Select the most recent released branch (you can select a beta release, ending with b1, b2, ... or even the "tip" if you want to live more dangerously). As of 2013 Jan 5, there is no released branch, and the most recent beta release is the one to get. A version is installed on the lab machines at C:\ProgramFiles\DataLogger. Documentation is downloaded with the source and is also available on the class web page.

To run the data logger, you will need an Arduino development environment (for downloading code to the Arduino board) and Python2.7 or Python3.3 with PySerial for communicating with the board.

The Arduino development environment is free from http://arduino.cc/en/Main/Software and should be downloaded onto any computers you wish to use. It is already on the lab machines in C:\ProgramFiles\arduino-1.0.3

Either Python 2.7 or Python3.3 can be used with the Data Logger code, but you need to install the PySerial module—this is the only non-standard module needed (Tkinter, which is also used, is part of the standard Python library). Note: Mac OS X often comes with an ancient version of Python, so you are likely to need to update your Python. See the documentation at python.org

We'll be doing plotting and model-fitting examples with gnuplot. You can choose to use other tools if you are more familiar with them and have sufficient mastery of them to fit complex functions and produce good-looking graphs. Gnuplot can be downloaded from the http://www.gnuplot.info/ website, but installation on Macs is sometimes tricky. See the post and comments on Karplus's blog about installing gnuplot on a Mac. The comment by Chuy is probably the most useful.

Text books

To offset the high parts cost, we'll be using only free on-line material for the textbook.

Wikipedia pages

We've identified a number of useful Wikipedia pages and collected them at http://en.wikipedia.org/wiki/User:Kevin_k/Books/applied_circuits
Of course, Wikipedia often has several different pages on a given subject, and we may not have found the most appropriate ones for the class—so we'd appreciate any pointers to other Wikipedia pages that are relevant to the class that you think we should share. We'll generally be using these pages as the primary textbook, but because they are encyclopedia articles, not a coherent textbook, there will often be times when the available articles are not tutorial enough (or not detailed enough). When that happens, you'll want to consult other on-line (and paper) resources.

All About Circuits

This is supposedly a somewhat slow-paced introduction to electronics that makes few assumptions about what you already know. The format, as 100s of HTML files, is a bit awkward to read, but fairly easy to search with Google (by adding "site:allaboutcircuits.com" to the keywords in the search box), so indexing is not really an issue. The book starts at about a middle-school level, but gets up to the beginnings of circuit theory. The Operational amplifier chapter looks usable, though it does not have a design focus—circuits are presented as almost magical rather than carefully analyzed from first principles (as is done in more theoretical circuits books) or from design rules of thumb (as is done in books like Horowitz and Hill).

Socratic Worksheets

The author of All About Circuits has also made available a number of worksheets with electronics problems on them at the Socratic Electronics Project Not all the problems are relevant to this course, but it should b fairly evident which are and which aren't. We may assign some of these, but you are encouraged to try them on your own whether or not we assign them.

Wayne Storr's Electronics Tutorials

http://www.electronics-tutorials.ws/ has a number of tutorials that are supposedly faster paced than the All About Circuits ones.

MIT's circuits course

If you prefer video lectures and lecture notes to books, you may find the lectures in the circuits course at MIT to be useful. Based on the course description, this is a rigorous traditional circuits course, having a bit more material than EE101 at UCSC. We'll be doing a little less theory and more hands-on stuff, and our order of material is quite different, so it is not a great fit for our course, despite the prestige of the MIT branding.

Texas Instruments' Op Amps for Everyone

TI's Op Amps for Everyoneduplicates some of the material in the Wikipedia book, but provides more detail and a cleaner presentation of some of the op-amp material. TI publishes it for free, in order to encourage engineers to design using the parts they sell.

Analog Devices' Op Amp Applications Handbook

The Op Amp Applications Handbook by Walter Jung, is published free by Analog Devices. Most of it is far too advanced for this course, but Sections 1-1 and 1-4 may be useful.

Complex number tutorials

If your understanding of complex numbers is rusty, and you get confused by our frequent use of them for talking about sine waves, then you might want to check out Wise Warthog's recommended complex number tutorials.

Other free on-line books

E-books directory has a collection of pointers to free on-line electronics books. If you find that one of these is at the right level for the course, let us know—a quick look suggested that several might be suitable, but none were a perfect fit.

Horowitz and Hill

A classic electronics text that fits the flavor of this course (though it covers much more) is Horowitz and Hill's Art of Electronics. Horowitz and Hill have one of the best explanations of op amps that I've read. The chapters relevant for this course are mainly Chapters 1 and 4.
Although the book was published in 1989, it is still a popular book, and even used copies are fairly expensive. The theory and design tips are still good, but the specific parts mentioned are mostly long gone. The authors have been promising a 3rd edition for years, but don't hold your breath—they're never going to catch up to the rate of change in digital electronics, so until they drop that half of the book, they'll just fall further an further behind schedule.

Other books

Wise Warthog reviews a number of other practical analog electronics books. His list is a good place to start if you want a hard-copy book.

Data and gnuplot scripts for loudspeaker modeling:

The lectures on Wed 2013 Feb 13 and Fri 2013 Feb 15 for inductors and loudspeaker modeling, used the following data and gnuplot scripts:

• 10W-loudspeaker-47ohm.data
• 10W-loudspeaker-47ohm-more.data
• inductor.gnuplot
• loudspeaker.gnuplot

Labs

Guidelines for lab write-ups

1. Thermistor feedback from grading the lab
2. Microphone feedback from grading the lab
3. Electrodes (no general feedback, just individual)
4. Hysteresis and capacitance touch sensor
5. Audio amplifier
6. FETs and phototransistors
7. Sampling and aliasing
8. Pressure sensors and instrumentation amplifiers
9. Power amp (class D) Power amp addendum
10. one-channel EKG

Each lab will be done with a different partner (and occasional singletons). There should be no repeat pairings. Prelab work should be done separately, but postlab work can be done together or separately.

Lab reports can be turned in either on the following Monday, with feedback by Thursday or Friday (before the next lab is written up), or the following Wednesday, with feedback the Monday after that.

Homework

Academic Integrity

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 we 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 lab assignments is expected, even required—but that doesn't remove the requirement to acknowledge the collaboration.

Classroom Accommodations for Disabilities

SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

BME194 Winter 2013

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