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(Last Update: 2020 December 21 10:50 PST )
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/
The biggest change this quarter is the switch to at-home labs. The other big change is a switch from in-person live lectures in which I mainly answer student questions to pre-recorded videos. This change was forced by my accepting funding and assistance from the university on converting the course—they were only willing to support conversion to asynchronous courses, not synchronous lectures.
Without student questions and student feedback, the video lectures are likely to miss things that you need explained, as I can't anticipate and cover all possible misunderstandings. Please use the Piazza forum to ask questions. If there is a common confusion, I'll try to add a new short video, in addition to answering questions on the forum.
Neither the video nor the forum are substitutes for reading the book—both are supplemental.
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. Having names turned on for all Zoom meetings may help—please don't confuse me by using someone else's account or name.
Students will be able to
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.
BME 51B is still a 5-unit course, which means that 15 hours a week of work are expected. Here is a rough breakdown of the hours:
| hours/week | activity |
|---|---|
| 1.2 | video lectures |
| 4 | lab |
| 3 | reading |
| 1.9 | homework |
| 4.9 | pre-lab and lab writing |
We do not have class discussion sections, but we do have required labs (2 hours attendance required a week). Questions are welcome during lab times, as well as office hours. If you want to communicate with the group tutors (if we have any), your fellow classmates, or the instructor, please use the Piazza forum https://piazza.com/ucsc/fall2020/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.
Use e-mail to karplus@soe.ucsc.edu for personal questions (absence, illness, DRC accommodations, … ), not for questions about course content, due dates, or other items of potential interest to classmates. Misdrected questions will be answered on Piazza anyway.
Most of the tools and parts are carried over from BME 51A, but a few new ones (about $25 worth) are partly covered by the course lab fee for this quarter and will be mailed to you before the quarter starts. Some new parts and equipment, forced by the change to at-home format that does not allow easy sharing, are not covered by the approved lab fee (nor are the shipping costs)—we are hoping that the University will use some of the COVID funds to cover this additional expense.
Because of the switch to at-home labs, we will need to ship you some loaner equipment (Analog Discovery 2, power supply, stainless-steel electrodes, Ag/AgCl electrode holder), that you need to ship back at the end of the quarter. We cannot ship the heavy soldering stations for a reasonable price, so are planning to include low-cost pencil irons in the tool kit. We have sent email to students asking if they already have their own soldering setups or Analog Discovery 2s, so that we can save on shipping costs. (Also, Analog Discovery 2 units are in very short supply worldwide, and they are needed for other classes as well.)
You must register for the class before 2020 September 7, so that there is time to ship your parts and tools to you.
The list of parts can be found at https://gasstationwithoutpumps.wordpress.com/parts-and-tools-bme-51b-fall-2020/
To offset the high parts cost, we'll be using only free online material for the textbook.
The book is a fairly large file (23.4 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. There are updates from version used in Winter 2019, including changes to the electrode lab, so make sure you pick up Edition 1.1 from September 2020.
As in previous years, I will give 25¢ for the first report of any error in the book (even minor typos). All errors need to be reported on our Piazza page.
You should watch the videos just after reading the corresponding section of the book—they are a supplement to the book, not a replacement for it.
I am also creating videos for BME 51A, for those of you who would like to review material from the previous course.
Because these videos are new and I'm just learning to make lecture videos, I expect a lot of rough spots and problems with them. I will award 25¢ for the first report of each major error in the videos (not minor stumbles or awkward transitions, but errors of content and incorrect closed captioning for videos that have had the captions edited—not the autocaptioning). All errors need to be reported on our Piazza page.
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.
Students are expected to have a laptop or desktop computer with two USB-A ports for labs (one for the Analog Discovery 2 and one for PteroDAQ). 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 loaned to students, but students can also buy their own (except for Digilent's running out due to the difficulty getting the components from Analog Devices) 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.
Data-acquisition software was developed specifically for this course and is available from https://github.com/karplus/PteroDAQ under the "Code" button. If you already use GitHub Desktop, you can use that to download the code, otherwise download the ZIP archive and uncompress the archive. Documentation is downloaded with the source, but only the installation is reasonably documented right now. See https://github.com/karplus/PteroDAQ/blob/master/Installation.md for 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:
The biggest change this quarter, forced by the COVID-19 pandemic, is moving the labs from Baskin Engineering to at-home labs. We will still have scheduled lab times, for which I will try to set up breakout rooms on Zoom, so that you and your partner can meet and can ask for help together. When no one is asking for help, I'll float from room to room, looking over people's shoulders. This will probably be a poor substitute for help available in the in-person labs, though you will be doing essentially the same activities as you would have then.
For the lab sessions, you will need video links, so that help can be given with hardware debugging—I'll need to be able to see the hardware being worked on, and you'll have to be able to share schematics and other design notes with me and with your partner.
The labs are contained in the textbook, rather than as separate lab handouts. Almost the entire book 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, if we have an odd number of students). 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 and yourre partner by e-mail at least twelve hours before the deadline, so that the group can be split. Otherwise only the last submitted report for the group will be graded.
| Dates | Lab |
|---|---|
| Thurs 1 Oct 2020–Wed 7 Oct 2020 | Lab 7: Electret microphones |
| Thurs 8 Oct 2020–Wed 14 Oct 2020 | Lab 8: Loudspeakers |
| Fri 16 Oct 2020 | Lab 7+8 report due |
| Thurs 15 Oct 2020–Thurs 29 Oct 2020 | Lab 9: Microphone preamp |
| Lab 9 report due | |
| Mon 2 Nov 2020–Fri 6 Nov 2020 | Lab 10: FETs |
| Mon 9 Nov 2020–Tues 17 Nov 2020 | Lab 11: Class-D power amp |
| Fri 20 Nov 2020 | Lab 10+11 report due |
| Wed 18 Nov 2020–Tues 1 Dec 2020 | Lab 12: electrodes |
| Fri 4 Dec 2020 | Lab 12 report due |
| Wed 2 Dec 2020–Fri 11 Dec 2020 | Lab 13: EKG |
| Tues 15 Dec 2020 (4 p.m.) | Lab 13 report due |
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.
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.
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 set the grading mechanism to be just point accumulation.
| work | total points available |
|---|---|
| final design reports | 400 |
| pre-lab drafts of design reports | 82 |
| 10 quizzes | 60–80 |
| other homework | 35 |
The grading scale for each of the five design reports will be
| letter grade | points |
|---|---|
| A | 80 |
| A- | 73 |
| B+ | 67 |
| B | 60 |
| B- | 53 |
| C+ | 47 |
| C | 40 |
| C- | 33 |
| D+ | 27 |
| D | 20 |
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 initial points given on Canvas for assignments are tentative and may be changed when we do the grading.
All submissions (for homework, pre-lab drafts, reports, and quizzes) must be done on Canvas as single PDF files. Only the most recently submitted file will be graded. Files sent via e-mail will be ignored.
Quizzes, homework, and pre-lab drafts will not be accepted late and cannot be redone for credit.
There will be some short quizzes, to check that students have done the reading. These should be similar to the homework (which is easier than the pre-lab drafts). Collaboration is not allowed on the quizzes.
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 and homework.
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. There are approximately 587±10 total points available. Here is an approximate guide to the major breakpoints in scoring (to be replaced when final thresholds are set):
| letter grade threshold | total points |
|---|---|
| A-/B+ | approx 514 (87.5%) |
| B-/C+ | approx 367 (62.5%) |
| C/C- | approx 257 (43.75%) |
I set the thresholds based on 622 points (not including the 4 bonus points for completing the SETs), then lowered thresholds by a few points to get round numbers, to put the thresholds in bigger gaps between adjacent totals, and to bump a few people up a level. The thresholds on the original syllabus were set based on a smaller total number of points—the quizzes ended up with more points than originally planned, partly because of the change to open-book, open-notes quizzes.
| letter grade threshold | default | threshold used |
|---|---|---|
| A-/B+ | 544.3 | 530 |
| B+/B | 505.4 | 500 |
| B/B- | 427.6 | 420 |
| B-/C+ | 388.8 | 380 |
| C+/C | 349.9 | 340 |
| C/C- | 272.1 | 270 |
| C-/D+ | 233.3 | 230 |
| D+/D | 194.4 | 190 |
| D/D- | 116.6 | 110 |
The homework schedule is still somewhat tentative, due to the change to online teaching and the different structure of Fall quarter from Spring quarter. Homework, pre-lab reports, and lab reports will all be turned in as PDF files through Canvas. The deadline will be 11:00 a.m. (Pacific Time) on the due date (unless otherwise noted). Assignments are due in the morning, not late at night (except for those of you in distant time zones).
Videos on the Applied-Analog Electronics channel corresponding to the required reading should also be viewed before the due date of the reading.
There will be a 3-hour grace period for late submissions, but you should submit something before the deadline, even if you replace it during the grace period. If you need an extension on a assignment, request it at least twelve hours before the deadline, with a strong argument for the necessity—just leaving things until the last minute is not a sufficient excuse.
| Due | Read before class or lab | Turn in before 11 a.m. (Pacific Time) |
|---|---|---|
| Fri Oct 2 | Chapter 26 (microphones), Lab 7 | HW 1: 26.1–26.6. Pre-Lab 7.1–7.3 |
| Mon Oct 5 | Chapter 28 (inductors), 29 (loudspeakers) | HW 2: 26.7, 26.9. |
| Wed Oct 7 | Lab 8 (loudspeaker modeling) | Pre-Lab 7.1–7.5 HW 3: 28.1, 29.1–29.6 |
| Fri Oct 9 | Pre-Lab 8 | |
| Mon Oct 12 | Lab 9 (audio amp) | |
| Wed Oct 14 | Chapter 32 (Field-effect transistors) | Pre-Lab 9 |
| Fri Oct 16 | Lab 7+8 report (microphones and loudspeakers) | |
| Mon Oct 19 | Chapter 33 (comparators) | |
| Wed Oct 21 | Lab 10 (Measuring FETs) | HW 4: 32.1–32.3 |
| Fri Oct 23 | Sections 35.1–35.6 | |
| Mon Oct 26 | Sections 35.7–35.10 | |
| Wed Oct 28 | HW 5: 35.1–35.6 | |
| Fri Oct 30 | Lab 11 (power amp) | |
| Sat Oct 31 | Lab 9 report (preamp) | |
| Mon Nov 2 | Lab 7+8 rewrite (for those with C-) | |
| Wed Nov 4 | ||
| Fri Nov 6 | Chapter 38 (Electrodes) | Pre-Lab 11 (Class-D amplifier) |
| Mon Nov 9 | Lab 12 (electrodes) | |
| Wed Nov 11 | Veterans' Day | |
| Fri Nov 13 | Chapter 40 (instrumentation amps) | HW 6: 38.1–38.3 |
| Mon Nov 16 | ||
| Wed Nov 18 | Pre-Lab 12 (electrodes) | |
| Fri Nov 20 | Chapter 41 (EKGs) | Lab 10+11 report (FETs and Class D) |
| Mon Nov 23 | Lab 13 (EKG) | HW 7: 40.1–40.3 |
| Wed Nov 25 | Pre-Lab 13 (EKG) | |
| Fri Nov 27 | Thanksgiving holiday | |
| Mon Nov 30 | ||
| Wed Dec 2 | ||
| Fri Dec 4 | Lab 12 report (electrodes) | |
| Mon Dec 7 | ||
| Wed Dec 9 | ||
| Fri Dec 11 | ||
| Tuesday 15 Dec | Final exam time: 4–7 p.m. probably not used. | 4 p.m. Lab 13 report (EKG), final deadline for all work. |
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| 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