(Last Update: 2019 June 17 13:33 PDT )

Instructor and Assistant(s)

• Kevin Karplus Office: Physical Sciences Building 318, Office hours: (tentative) Tues 1:30–2:30, Fri 12:40–1:40
  karplus@soe.ucsc.edu
• Teaching Assistant: None
• Piazza forum for discussions: https://piazza.com/ucsc/spring2019/bme51b/
  The Piazza page is the preferred way to ask questions (except for personal items like illness or disability accommodations).
• Class meetings: Thimann 1 4:00–5:05
• Lab meetings: Baskin Engineering 115 and 150)
  TTh 3:20–4:55 (Section 1) tutors: Daniel Brenner dabrenne@ucsc.edu and Amr Makhamreh amakhamr@ucsc.edu
  TTh 5:20–6:55 (Section 2) tutors: Ali Fallahi afallahi@ucsc.edu and Todd Nabonne tnabonne@ucsc.edu
• Graders: Ali Fallahi and Jonathan Nguyen
• Final exam time: Tuesday June 11 7:30–10:30 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 there have been major rewrites of the textbook this year with some changes to the labs, 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.

Names and pronouns

The pronouns "he, him, his" are best when referring to me in the third-person. It is acceptable to address me as "Kevin", "Professor", "Professor Karplus", but not as "Dr. Karplus" (I have a Ph.D., not an M.D., and prefer not to use "Doctor" as a title).

Although I will attempt to learn student names and pronouns, I have much lower than average ability at remembering names and faces. It will be surprising if I manage to learn and retain more than one name a week. Please do not be offended if I get your name or preferred pronoun wrong---my disability with names and faces is to blame, not any intention to insult.

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 biblatex.
• 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:

Class discussions

We do not have class discussion sections, but we do have required labs (2 meetings a week). Questions are welcome during lecture and lab times, as well as office hours. If you want to communicate with the group tutors, your fellow classmates, or the instructor, you can use the Piazza forum https://piazza.com/ucsc/spring2019/bme51b/home.

The Piazza forum will also be used for communications from the instructor or group tutors to the class—particularly for changes to due dates, assignments, or other urgent materials. Set up Piazza to e-mail you when there are updates, and check Piazza daily.

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-2019/

Text books

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

Applied Analog Electronics

Note: students enrolled in the class got a free electronic copy of the textbook for 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 (26.9 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.

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.

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.

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. BELS has a few AD2's to rent, but with mechatronics being taught this quarter, they will probably have rented all they have before the quarter even starts.

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. Documentation is downloaded with the source, but only the installation is reasonably documented right now. See https://bitbucket.org/abe_k/pterodaq/wiki/Home for more information, including installation instructions.

To run the PteroDAQ data-acquisition system, you will need Python2.7 or Python3 (3.4 or newer). Note: Mac OS X often comes with an ancient version of Python, so you are likely to need to update your Python. 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.) Gnuplot can be downloaded from the http://www.gnuplot.info/ website, but installation on Macs is sometimes tricky---there are instructions in the textbook.

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.overleaf.com, which allows collaboration between authors. A template for lab reports (which can be used with stand-alone LaTeX or overleaf.com) is available at https://www.overleaf.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.

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 "pre-lab"), one due after the lab. The first draft should be a joint effort of the two partners—the second usually will be also, but partners can decide to submit separate reports (generally a recognition of a failed partnership).

If you want to submit separate pre-lab or lab reports, you must inform Kevin Karplus by e-mail at least 8 hours before the deadline, so that the group can be split. Otherwise only the last submitted report for the group will be graded.

Lab rules: No open food or drink in the lab! This includes coffee and tea cups with snap-on lids. Leave your food and drinks in Jack's Lounge, just outside the lab doors.

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.

Read Section 7.13 (Citation) of the textbook twice, to be sure you understand the rules.

Collaboration without explicit written acknowledgment when the assignment is turned in 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

Officially approved DRC notification:
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 me privately during my office hours or by appointment, preferably within the first two weeks of the quarter. At this time, I would also like us to discuss ways we can ensure your full participation in the course. I encourage all students who may benefit from learning more about DRC services to contact DRC by phone at 831-459-2089, 459-4806 (TTY), or by email at drc@ucsc.edu.

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 grade book 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 be graded on a similar scale as the lab reports, but scaled to a different total. They will vary in weight, depending on how long and difficult they are. The weights given on Canvas are tentative and may be changed.

The homework will be weighted approximately 1 point per question—the points given on Canvas are tentative and may be changed.

Quizzes, homework, and pre-lab drafts will not be accepted late and cannot be redone for credit.

There will be some short in-class quizzes, to check that students have done the reading. These should be similar to the homework (which is easier than the pre-lab drafts).

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

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 approximately 600 total points available. Here is an approximate guide to the major breakpoints in scoring (to be replaced when final thresholds are set):

Final grade thresholds

I set the thresholds based on 579 points (treating the homework as purely bonus points), then lowered thresholds by a point or so to put the thresholds in the bigger gaps between adjacent totals.

Homework

Homework schedule is still somewhat tentative, due to the rewrite of the book and changes in the lab schedule. 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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Biomolecular Engineering Department

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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