(Last Update: 2018 June 19 18:22 PDT )

Instructor and Assistant(s)

• Kevin Karplus Office: Physical Sciences Building 318, Office hours: W 1:30–3, Th 3–4:30 karplus@soe.ucsc.edu
• Teaching Assistant: None
• Piazza forum for discussions: https://piazza.com/ucsc/spring2018/bme51b/home The Piazza page is the preferred way to ask questions (except for personal items like illness or disability accommodations).
• Class meetings: Thimann 1 10:40–11:45
• Lab meetings: Active Learning Classroom (Science and Engineering Library)
  TTh 5:20–6:55 (Section 1) tutors: Andy Baldovino, William Van Hyning
  TTh 7:10–8:45 (Section 2) tutors: Henry Hinton, Jason Prince
• Graders: Henry Hinton, Jason Prince
• Final exam time: Monday June 11 4–7 p.m. (may not be used)

Overview

The course is the continuation of BME 51A, which is the sole prerequisite.

The theme for both courses is "connecting real-world signals to computers using analog electronics", with the emphasis in BME 51B being on higher frequency and higher power amplifiers, and more complicated modeling of transducers.

Currently, the best description of the course is in the textbook written for the course, but students interested in how the course evolved may be interested in the posts on Prof. Karplus's blog:
http://gasstationwithoutpumps.wordpress.com/circuits-course-table-of-contents/

Because the course had a major rearrangement of the material last year and change of pace in switching from one intense quarter into two quarters, with major rewrites of the textbook this year, 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.

Learning outcomes

Students will be able to

• draw useful block diagrams for amplifier design.
• use simple hand tools (screwdriver, flush cutters, wire strippers, multimeter, micrometer, calipers, ... ).
• hand solder through-hole parts and SOT-23 surface-mount parts.
• use USB-controlled oscilloscope, function generator, and power supply.
• use python, gnuplot, PteroDAQ data acquisition system, and Waveforms on own computer.
• do computations involving impedance using complex numbers.
• design single-stage high-pass, band-pass, and low-pass RC filters.
• measure impedance as function of frequency.
• design, build, and debug simple op-amp-based amplifiers.
• draw schematics using computer-aided design tools.
• write design reports using LaTeX and BibTeX.
• plot data and theoretical models using gnuplot.
• fit models to data using gnuplot.

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.

Hours expected

BME 51B is now a 5-unit course, which means that 15 hours a week of work are expected. Here is a rough breakdown of the hours:

What to buy

Tools and Parts

Most of the tools and parts are carried over from BME 51A, but a few new ones (about $18 worth) are covered by the course lab fee for this quarter and will be issued on the first day of lab. Dropping the course does not result in a refund of lab fees if you have already gotten the tools and parts.

The list of parts can be found at https://gasstationwithoutpumps.wordpress.com/parts-and-tools-list-for-bme-51b-spring-2018/

Software

Students are expected to bring a laptop with two USB-A ports to labs (one laptop suffices for each pair of lab partners, but it is often best for each student to have their own). Computers will not be provided in the labs. All software is the same as in BME 51A and will run on Windows, Mac OS, or Linux: Waveforms 3 (for Analog Discovery 2 oscilloscope, function generator, and power supply), PteroDAQ, Python (with scipy), and gnuplot.

The Analog Discovery 2 hardware will be available in the lab, but students can also buy their own for use at home from http://store.digilentinc.com/analog-discovery-2-100msps-usb-oscilloscope-logic-analyzer-and-variable-power-supply/. If you choose to buy one, be sure to get the academic pricing (a 36% savings). You'll need a power supply as well---I recommend the Meanwell SGA12u05-P1J (5V 2.4A) supply, which fits well in the box with the USB oscilloscope.

I recommend the Anaconda Python distribution (see https://anaconda.org/anaconda/python and https://docs.anaconda.com/anaconda/install/), which loads a lot of Python modules that are useful, like NumPy, SciPy, and MatPlotLib. 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 complicated functions that involve complex-number arithmetic and to produce good-looking graphs, but no help will be available for systems other than gnuplot. (Excel is not acceptable plotting software.)

All pre-lab and lab reports will need to be prepared with LaTeX. You can either install your own stand-alone copy of LaTeX (see https://www.latex-project.org/get/) or use https://www.sharelatex.com, which allows collaboration between authors. A template for lab reports (which can be used with stand-alone LaTeX or sharelatex.com) is available at https://www.sharelatex.com/project/596b60947639ba5d59e0874f.

Additional scripts written specifically for the course:

• definitions.gnuplotUseful definitions in a gnuplot script for Bode plots and impedance modeling
• 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. You will need to make some modifications to this program for processing EKG signals.

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 got a free electronic copy of the textbook from BME 51A, 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 (23 MBytes), so I recommend keeping a copy on your laptop, rather than trying to download 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. There may be a new release during Spring break, in which case you would need to download the PDF file again for BME 51B.

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.

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.

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 available. 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 across both quarters. Each lab report will be done in two drafts: one due before the lab (the "prelab"), one due after the lab. The first draft should be a joint effort of the two partners, and the second usually will be also, but partners can decide to submit separate reports (generally a recognition of a failed partnership).

Lab rules: No open food or drink in the lab! This includes coffee and tea cups with snap-on lids. The only drinks allowed are those that will not spill at all if knocked over.

Clothing in the lab is unrestricted, except on days when we do soldering. On those days, you should wear long pants and cotton clothing, to avoid burns from spattered solder. Safety goggles (provided in lab) are also required while soldering.

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

If you qualify for classroom accommodations because of a disability, please submit your Accommodation Authorization from the Disability Resource Center (DRC) to Prof. Karplus in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY).

Evaluation

Students will be graded primarily on the five design reports, due biweekly, but there will also be points for quizzes, homeworks, and the pre-lab drafts.

Don't trust the Canvas summary of your grade—use only the total number of points collected. Because the Canvas gradebook has no clean mechanism for any grading scheme except accumulation of total points, I have recast the grading mechanism to be just point accumulation.

The grading scale for each of the five design reports will be

The pre-lab reports will vary in weight, depending on how many questions the pre-lab needs to answer (about 3 points per question, adjusted for the difficulty of the questions). The homework will be weighted approximately 1 point per question.

Homework and pre-lab drafts will not be accepted late.

Because of the size of the class and the grading bandwidth, assignments cannot be redone to get a higher grade.

The grading standard for the design reports is expressed as points, but is not really "point-based"—I'm not looking for specific items and taking off points if they are wrong or missing. Instead the grading is holistic, taking into account all aspects of the writing. A good report that covers all the main ideas of an assignment earns a B. If it is very well written, it gets a B+. Extras beyond the essentials can raise the report to an A-, or (if exceptionally good) an A, but the essentials must be correct and clear before extras add anything to a report.

Poor writing can lower a complete report to a B- or lower. Parts that are missing, inconsistent, or wrong will lower the grade further. Inconsistently reported component values or serious errors in the schematic may be enough by themselves to reduce the grade below passing.

The interpretation of the total points will be adjusted somewhat based on the exact number of points available and how difficult the quizzes and homeworks turn out to be (many of the questions are new this year). There are 600 total points available. Here is an approximate guide to the major breakpoints in scoring (to be replaced when final thresholds are set) based on 590 total points (the C/C- number seems to be based on the D+/C- threshold, not the C-/C threshold):

The final point thresholds, both initial estimates from percentage of points and final thresholds after adjustment:

Homework

The homework schedule is still somewhat tentative, due to the rewrite of the book, the change in pacing for the course, and the increased grading for the larger class. Homework, pre-lab reports, and lab reports will all be turned in as PDF files through Canvas. The deadline will be 11:59 p.m. on the due date (unless otherwise noted).

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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