(Last Update: 2017 June 5 15:10 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 110, MWF 10:40–11:45
• Lab meetings: Baskin Engineering 150, TTh 1:30–3:05 (Section 1) Group tutor: Will Van Hyning wvanhyni@ucsc.edu
  TTh 3:20–4:55 (Section 2) Group tutor: Alexander Martin-Ginnold amarting@ucsc.edu
  TTh 5:20–6:55 (Section 3) Group tutor: Henry Hinton hhinton@ucsc.edu
• Final exam time: Thursday, 2017 June 15, 4–7 p.m.

Overview

BME 51B is open to anyone who has passed BME 51A, but should be taken immediately afterwards, as the division of the material between the two parts may change from year to year.

The theme for the course is "connecting real-world signals to computers using analog electronics". The second part, BME 51B, will concentrate mainly on characterizing sensors and transducers (including non-linear models) and on amplifier design. We will work with microphones, loudspeakers, and electrodes this quarter.

Most of the basic concepts were covered in BME 51A—this quarter will concentrate on applying those concepts and gaining facility in using them for design. New concepts include inductors and pulse-width modulation. We will also revisit band-pass filtering.

What to buy

Tools and Parts

This quarter uses the tools and parts acquired in BME 51A, plus a few new parts. The new 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 parts.

Software

We will continue to use PteroDAQ, available free 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, but you are much better off using your own laptops. Documentation is downloaded with the source, but only the installation is reasonably documented right now. You'll need Python installed: I recommend the Anaconda distribution, as it loads useful modules, like NumPy and SciPy.

We'll continue doing plotting and model-fitting examples with gnuplot. Gnuplot can be downloaded from the http://www.gnuplot.info/ website, but installation on Macs is sometimes tricky. See the post, which has updated instructions at the end of the post.

• boilerplate.gnuplotBoilerplate gnuplot script for impedance modeling
• definitions.gnuplotUseful definitions in a gnuplot script for Bode plots and impedance modeling (more stripped down than boilerplate.gnuplot)
• Filter program for doing band-pass 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.
• example.tex a short example of the use of LaTeX, with output in example.pdf.
• subfigure-snippet.tex is a short piece of the source code for the sampling chapter, showing how a figure with subfigures can be created. It requires the "subcaption" package.
• preamble-snippet.tex has part of the preamble for the book (the part between \documentclass and \begin{document}), showing a few of the packages used, the adjustment to \floatpagefrac and other parameters to handle having lots of figures, and the macros for doing consistent cross-references. I cut out a lot of the complexity of the preamble, and I may have removed a package necessary for what I've left.
• http://users.soe.ucsc.edu/~karplus/bme101/pc-boards/op-amp-proto-rev0/op-amp-proto-rev0-worksheet.pdf Worksheet for doing layouts on the op-amp protoboard

Text books

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

Applied Electronics for Bioengineers

We will continue to use this text, but students should download a new copy (released 2017 April 2), as it contains new material on band-pass filters and some new exercises.

I have been writing this book specifically for this class, and it is not quite done. I don't expect any updates during the quarter, but I will frequently solicit suggestions for additions or improvements needed. Students will be able to download any future editions that I distribute through LeanPub for free—the LeanPub model is designed for work-in-progress books.

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.

LaTeX references

• LaTeX User's Guide and Reference Manual Leslie Lamport. This is a generally useful reference and I recommend keeping a copy handy for working on your thesis proposal and thesis. You can now find almost all the material from the book on-line, so it may no longer be necessary to have a physical copy.
• Art of Problem Solving LaTeX tutorial
• One student recommended this reference: http://en.wikibooks.org/wiki/LaTeX

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. Students who do not attempt the homework ahead of time are doing their lab partners a major disservice and take up too much of the group tutor and instructor time in the lab, hurting everyone else in the section.

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, including the pairings from BME 51A. Pre-lab work should be done separately, but post-lab work can be done together or separately. A detailed design report will be required for each lab.

Change this quarter:All design reports will be required to be done using LaTeX—documents produced with Word will not be accepted. There will be some instruction in LaTeX and BibTeX. A number of students have found the sharelatex site https://www.sharelatex.com/ to be useful for collaboration on documents—it is free for two people working together.

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.

Design reports are expected to be entirely the work of the two partners on the project. Copying block diagrams, schematics, or other elements of the report is not acceptable, even if acknowledged.

Classroom Accommodations for Disabilities

UC Santa Cruz is committed to creating an academic environment that supports its diverse student body. If you are a student with a disability who requires accommodations to achieve equal access in this course, please submit your “Accommodation Authorization Letter” from the Disability Resource Center (DRC) to Prof. Karplus privately during office hours or by appointment, as soon as possible in the academic quarter, preferably within 1 week. I also am open to and want to encourage you to discuss with me ways we can ensure your full participation in this course. If you have not already done so, I encourage you to learn more about the many services offered by the DRC. You can visit their website (http://drc.ucsc.edu/index.html), make an appointment, and meet in-person with a DRC staff member. You can also reach them by phone +1-831-459-2089, 459-4806 (TTY), or email drc@ucsc.edu

Evaluation

Students will be graded primarily on the five design reports, due weekly. The pre-lab homework combined will be worth about one design report. Homework will not be accepted late and cannot be redone for credit.

In addition there may be one or two quizzes, each with weight equal to one of the design reports. The need for quizzes will be determined mainly by how diligent students are about doing the pre-lab design work.

Lab reports that get a grade of C+ or lower can be redone once, with a new due date a week after the reports are returned to the class. (Being absent when reports are returned does not extend the due date.) Those with a grade of "REDO" must be redone, or they will be converted to "F". Grading standards are somewhat higher for redone reports, so that minor errors that would have been tolerated in a first draft will be judged more harshly in a redone report. All previously graded versions of the report must be turned in with any redone report.

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