(Last Update: 2017 March 13 09:01 PDT )

Instructor and Assistant(s)

• Kevin Karplus Office: Physical Sciences Building 318, Office hours: MW 4–5 karplus@soe.ucsc.edu
• Class meetings: Physical Sciences Building 114, MWF 2:40–3:45
• Lab meetings: Baskin Engineering 150, TTh 1:30–3:05 (Section 1) Group tutor: Will Van Hyning
  TTh 3:20–4:55 (Section 2) Group tutor: Henry Hinton
  TTh 5:20–6:55 (Section 3) Group tutor: Alexnder Martin-Ginnold
• Final exam time: Monday, 2017 March 20, 8–11 a.m.

Overview

The course is intended for sophomores and juniors in bioengineering with priority given to bioengineering majors, but is open to anyone who meets the prerequisites:

• Calculus (Math 19A or AP Calculus BC with 4 or 5)
• high-school physics (or Physics 5C or 6C)

Students considering the bioelectronics or assistive technology: motor concentrations should take BME 51A+B early (before EE 101/L), which may be difficult to schedule. Key for the motor concentration is getting CMPE 118 (Mechatronics) in fall of the junior year—scheduling should be designed to ensure that, even at the expense of non-optimal course ordering.

Note: starting in Winter 2017, Applied Electronics for Bioengineers is a sequence of two 4-unit courses, BME 51A (Winter) and 51B (Spring), rather than a 7-unit course plus lab in one quarter, to make the pace more manageable for both students and faculty, and to increase the capacity in the course, which is constrained by the number of lab hours needed a week.

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 microprocessors (note microphones and electrodes are in BME 51B, the rest in BME 51A). The signals we will be looking at will be related to physiological measurements (blood pressure, heart beat, and so forth), but the principles can be applied to many other measurements.

The old bioengineering curriculum (before the 2014–15 catalog) will accept BME51A+B as fulfilling the EE101/L (circuits) requirement, but EE will not be accepting it as a prerequisite for further electronics courses. The new (starting 2014–15) curriculum for bioengineers requires BME 51A+B for all concentrations, and EE 101/L in addition for the bioelectronics and assistive technology: motor concentration.

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—there is a more compact description in the textbook.

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—I tried to make the labs require design, not just cookbook procedures. The complexity of the design tasks should ramp up through the two quarters.

Because the course had a major rearrangement of the material and change of pace in switching from one intense quarter into two quarters, I will seek frequent feedback from the students in the course about improvements that can be made in the labs, the lectures, and the textbook.

What to buy

Tools and Parts

This year the parts and tools are covered by the course lab fees. There are about $70 worth of tools, parts, microcontroller board, and USB cable. These tools and parts will be provided in the first lab meeting, as we will be using them immediately. Dropping the course does not result in a refund of lab fees if you have already gotten the tools and parts.

We have ordered enough kits for the maximum enrollment in the course (plus a couple spares), so dropping after the kits have been issued does not open up many slots for more students. If you are not certain you are going to take the course this quarter, drop the course before the first lab on January 10, so that someone on the waiting list can join the course.

Software

Data acquisition software was developed specifically for this course, and is available from http://bitbucket.org/abe_k/PteroDAQ/downloads under the "Tags" tab. Select the "default" branch under the "branches" tab and download in zip, gz, or bzip2 archive format. A version is installed on the lab machines at C:\ProgramFiles\PteroDAQ. Documentation is downloaded with the source, but only the installation is reasonably documented right now.

To run the PteroDAQ data acquisition system, you will need Python2.7 or Python3. 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 or use the Anaconda Python, which loads a lot of Python modules that are useful. In particular, the filtering software in the SciPy package will be useful for digital filtering of heartbeat signals.

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, but no help will be available for systems other than gnuplot. 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.

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

• download for data acquisition software PteroDAQ should work under Windows, Mac OS X, and Linux, with either Python 2.7 or Python 3.4.
• Python (either 2.7 or 3.4) You can also use the anaconda or Enthought bundled versions of Python—these include extra useful packages like NumPy, SciPy, and MatPlotLib, which would require extra installation on the python.org distribution.
• gnuplot
• boilerplate.gnuplotBoilerplate gnuplot script for impedance modeling
• definitions.gnuplotUseful definitions in a gnuplot script for Bode plots and impedance modeling (more stripped down than boilerplot.gnuplot)
• Filter program for doing bandpass and low-pass filtering of PteroDAQ files—cutoff frequencies are built-in (suitable for pulse detection) to keep program short: bandpass-filter.py This program requires that NumPy and SciPy be installed in Python.

Text books

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

Applied Electronics for Bioengineers

Note: students enrolled in the class will be given a coupon for a free electronic copy of the textbook, including all subsequent updates published through LeanPub. I don't believe in requiring students to buy anything that I profit from.

The book is a fairly large file (18MBytes), so I recommend keeping a copy on your laptop, rather than trying to read it from the LeanPub site each time you need it.

I have been writing this book specifically for this class, and it is not quite done. If there is time, I will be rewriting or expanding portions of the book during the quarter, so you may need to download the PDF file more than once.

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).

In the early years (before my book draft), students found this the most useful of the on-line sources, as the tutorials assume no prior knowledge.

The author of All About Circuits has also made a number of video lectures and practice worksheets available. Not all the worksheets are relevant to this course, but it should be fairly evident which are and which aren't. I may assign some of these, but you are encouraged to try them on your own whether or not they are assigned.

Wikipedia pages

I'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 I may not have found the most appropriate ones for the class—so I'd appreciate any pointers to other Wikipedia pages that are relevant to the class that you think we should share. These pages should help fill in the gaps where my book does not cover information you need, 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.

In previous years, many students found the Wikipedia articles too difficult for them, though they are often a better reference than All About Circuits, allowing you to go deeper into the material.

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 more material than EE101 at UCSC. We'll be doing less theory and more hands-on stuff, and our order of material is very 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 Everyone duplicates 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 me 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, 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.
The second edition (1989) is still usable, though many of the parts described in the book are no longer usable. The third edition, released in 2015, is worth the money for those who plan to go further in electronics than just this course.

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.

Labs

The labs are contained in the textbook, rather than as separate lab handouts. The entire book is is required reading for BME 51A+B—the chapters provide essential understanding for the design work in the labs, and homework will be preparation for the labs.

It is essential to read the lab chapters and do the design work before coming to lab—this is a design class, not lab-demo class, so most of the writing and thinking has to happen before the lab time. Students in past years who did not have completed designs before lab generally wasted a lot of lab time doing pencil-and-paper work and had trouble getting their designs built and tested.

Each lab will be done with a different partner (and occasional singletons). There should be no repeat pairings. Pre-lab work should be done separately, but postlab work can be done together or separately. A detailed design report will be required for each lab (except Lab 1).

Academic Integrity

Anyone caught cheating in the class will be reported to their college provost (see UCSC policy on academic integrity for undergrads and for grad students), will fail the assignment, 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 lab assignments is expected, even required—but that doesn't remove the requirement to acknowledge the collaboration.

Classroom Accommodations for Disabilities

Evaluation

Homework

SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

BME51 home page

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