(Last Update: 2015 May 28 18:22 PDT )

Instructor and Assistant(s)

• Kevin Karplus Office: Physical Sciences Building 318, Office hours: W 3–5 karplus@soe.ucsc.edu
• Class meetings: Engineering 2, Rm. 194, MWF 12:30–1:40
• Lab meetings: Baskin Engineering 150, TTh 10–1 (Section 1) Group tutor: Edgar Valdez egvaldez@ucsc.edu
  TTh 2–5 (Section 2).
• Final exam time: Monday, 2015 June 8, 4–7 p.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 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)

Students considering the bioelectronics concentration should take BME 101/L early (before EE 101/L), which may be difficult to schedule because of the prereqs. Students who did well in high-school physics may request a waiver of the physics prereq, which may be granted if there is room in the course and the student is sufficiently convincing about their ability to handle the material.

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 (Arduinos or Freescale's KL25Z). The final lab will be the design, implementation, and testing of a small single-channel electrocardiogram (or electromyogram).

The old bioengineering curriculum (before the 2014–15 catalog) 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 some overlap in content. The new (starting 2014–15) curriculum for bioengineers requires BME 101/L 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.

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 quarter.

Although BME 101 is no longer a prototype but a regular course, I will seek frequent feedback from the students in the course about improvements that can be made. There are substantial changes from the previous two runs of the course, including a rescheduling of the labs and a new text.

What to buy

Tools and Parts

This year the parts and tools are covered by the course lab fees. There are about $80 worth of tools, parts, microcontroller board, and USB cable—the charged lab fee is $130, because the fee also covers wire, solder, printing, fuses for the ammeters, broken oscilloscope probes, and cost overruns from having to use UC-approved vendors (who often don't have the cheapest prices). I think that the lab fee is bigger than it needs to be, but BELS thinks it is too small (we have different views on how much extra should be in the budget beyond the parts kit itself). These tools and parts need to be obtained by 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.

Warning: the KL25Z 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. We will be soldering headers onto the KL25Z boards in the first week.

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:

• download for data acquisition software Note: this software has worked well under Python 3.4 on Mac OS X, but may have some trouble under Python 2.7.
• Python (either 2.7 or 3.4) You can also use the anaconda or Enthought bundled versions of Python.
• PySerial installation instructions
• gnuplot
• boilerplate.gnuplotBoilerplate gnuplot script for impedance modeling
• definitions.gnuplotUseful definitions in a gnuplot script for Bode plots and impdance modeling (more stripped down than boilerplot.gnuplot
• loudspeaker-low-pass-choose-C-power-law.gnuplot Script for choosing the capacitor in the LC filter for the power amplifier.
• Thermistor modeling: The script we developed in class on 2014 Apr 2 is at bme101-s14-therm1.gnuplot, with the output in bme101-s14-therm1.pdf. The more detailed script from 2013 is steinhart-hart.gnuplot. A much briefer script developed in class in 2015 is in thermistor-in-class.gnuplot, which produces thermistor-in-class.pdf
• Frequency detector program for capacitive touch sensor lab: freq_detector_own_isr.cpp freq_detector_own_isr_KL25Z.bin
• Echo program for echoing what is sent by the KL25 (only works on Mac OS X, because of the way that it opens the serial port): KL25-echo.py
• 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
• Worksheet for doing layout on the instrumentation-amp prototyping board: EKG-proto-rev3-worksheet2.pdf

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.

To run the data logger, you will need Python2.7 or Python3.4 with PySerial for communicating with the board. (Note: I've had some problems with Python 2.7 and PteroDAQ on Mac OS X, but it works fine with Python 3.4. )

Either Python 2.7 or Python3.4 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.

Draft of my book

I am writing a book specifically for this class and releasing the PDF of the latest draft to students in the class for free. Students will get a password for accessing the PDF file in class—please do not distribute the password or the PDF file to others. I will probably be rewriting 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 previous years (before my book draft), students found this the most useful of the on-line sources, as the tutorials assume no prior knowledge.

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 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 a bit more material than EE101 at UCSC. We'll be doing 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 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 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 (about $45). 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—apparently it will be released 2015 April 30 and can now be pre-ordered.

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 this year are contained in the textbook, rather than as separate lab handounts. 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.

Lab reports will be due at the beginning of class every Friday, starting with Lab 2 on sampling and aliasing. Labs 5 and 6 are in the same week, and will have a combined report, so there are a total of ten reports. I will endeavor to have lab reports graded and returned with detailed feedback in the next class (Monday).

Each lab will be done with a different partner (and occasional singletons). There should be no repeat pairings (unless the lab section has fewer than 11 students). Pre-lab work should be done separately, but postlab work can be done together or separately.

Read each lab chapter (twice) the day before the lab—there will often be pre-lab design work to do due on Mondays, and there won't be time during lab to do the design work. Some weeks have two lab chapters—read both the weekend before the labs and do the pre-lab exercises, so that you can ask questions on Mondays.

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 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

BME101 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