|
| SoE home |
|
| Kevin Karplus's home page |
|
| Biomolecular Engineering Department |
(Last Update: 2022 June 16 13:02 PDT )
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) or "Mr. Karplus".
Although I will attempt to learn student names and pronouns, I have much lower than average ability at remembering names and faces. On Zoom, with poor lighting and web cameras, I'm lucky if I recognize people whom I already know well. 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.
The course is a continuation of BME 51A, which is the only prerequisite.
Note: starting in Winter 2018, Applied Electronics for Bioengineers is a sequence of two 5-unit courses, BME 51A (Winter) and 51B (Spring), rather than two 4-unit courses (as in 2017) or a 7-unit course plus lab in one quarter (as in previous years), to reflect the workload experienced by the students, to make the pace more manageable for both students and faculty, and to increase the capacity in the course, which is constrained by the number of lab hours needed a week.
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 (note microphones and electrodes are in BME 51B, the rest in BME 51B). The signals we will be looking at will be related to physiological measurements (blood pressure, heart beat, and so forth), but the principles can be applied to many other measurements.
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/
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 now a 5-unit course, which means that 15 hours a week of work are expected for the median student. Here is a rough breakdown of the hours:
| hours/week | activity |
|---|---|
| 1.2 | video lectures |
| 1 | quiz |
| 4 | lab |
| 3 | reading |
| 1.6 | homework |
| 4.2 | pre-lab and lab writing |
We do not have mandatory class discussion sections, but we do have required labs (2 or 3 meetings a week). Questions are welcome during lab times, as well as during 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/spring2021/bme51b.
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.
This year the parts and tools are covered by campus funds (no lab fees allowed this year). These tools and parts will needed for the first lab meeting, as we will be using them immediately. If you drop the course, you must return the parts and tools.
The parts list for the quarter can be found at UPDATE!! PARTS LIST NOT POSTED YET https://gasstationwithoutpumps.wordpress.com/bme-51B-s2021-parts-and-tools/
Some tools are yours to keep at the end of the course—others are loaner items and must be returned at the end of BME 51B.
To offset the high parts cost, we'll be using only free on-line 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.
The most recent version of the book is the 2020 Dec 28 one, but I'm hoping to release a new version in March 2021, with minor bug fixes and additions. You should be fine reading the December edition, but pick up the new one once it comes out. I already gave coupons for free PDF copies of the book to everyone when they took BME 51A—you can get the current edition and all future updates of the book for free just by logging in to the LeanPub site.
I have been writing this book specifically for this class, and it is never quite done. I welcome corrections to the book. I will be paying at least 25 cents for the first report of anything I accept as being an error—more for more serious errors. Error reports should be done on the Piazza site for the course. (Students will be paid at the end of BME 51B.)
Watch a few of the soldering videos, then fill out the form for
soldering SOP (Standard Operating
Procedure), before the first lab session.
You are required to have completed the Standard Operating Procedure
(SOP) from UCSC Baskin Engineering Lab Support (BELS)
before you are allowed to solder:
https://forms.gle/BoeNs6KRdw9aN4Eg9
New (starting Fall 2020) is an Addendum to the Soldering SOP for soldering
remotely (i.e., at home). You need to read and digitally sign
the Addendum as well as the SOP:
https://forms.gle/9gWpuCXbf545xK3m9
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 won't assign these, but you are encouraged to try them on your own if you need more practice.
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 bring a laptop with two USB-A ports to labs The software will run on Windows, Mac OS X, or Linux.
The Analog Discovery 2 USB oscilloscope, function generator, and power supply that will be used in the labs is controlled by Waveforms 3, which is freely down-loadable from https://store.digilentinc.com/waveforms-previously-waveforms-2015/ The software can be run in "demo" mode without the hardware attached, which is useful for learning the many features of the software.
Students can (theoretically) 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 substantial savings). Unfortunately, AD2 units are still in short supply. 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 Documentation is downloaded with the source, but only the installation is reasonably documented right now (there is also documentation in the textbook).
To run the PteroDAQ data-acquisition system, you will need Python2.7 or Python3. 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 needed for digital filtering of heartbeat signals.
You can use the Python.org site Python (either 2.7 or 3.4 or newer). If you use python.org python, you'll have to install a number of the packages yourself.
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 if the gnuplot.info site does not provide a command-line-executable file.
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. There is a trick for getting collaboration without paying a license fee: sign someone else up (see https://www.overleaf.com/user/bonus). If you pass on your link to someone else in the class, when they sign up using it, you can have a collaborator on each of your projects. They can then post their link on Piazza, someone can use that, and so on. A few people will end up at the end of the chain(s)—they may have to get friends of family to sign up.
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
Software written specifically for the course—all of which is free:
I do not require you to turn on your camera for Zoom, but I find it much easier to work with people when I can see them, so I'd really prefer it if you had your camera on in lab breakouts and for office hours. Helping you debug hardware is also much easier if I can see the wiring, so having a good lighting and a camera that you can put your breadboard in front of really helps.
You should bring your laptop to every lab. It will need to have at least one and preferably two USB ports that can be connected to a USB micro-B connector (as data connections, not just power). You will use the laptop to communicate with the Teensy board running PteroDAQ (data-acquisition) software and with the Analog Discovery 2 USB oscilloscope/function generator/power supply/network analyzer/impedance analyzer.
Students in the class may make audio recordings and take photos for personal use (note-taking and review), but not share them with people not in the class, nor post the recordings or photos on the web or other social media.
Anyone caught cheating in the class will be reported to their college provost (see UCSC policy on academic integrity for undergrads), 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 providing a safe learning environment that is free of all forms of gender discrimination and sexual harassment, which are explicitly prohibited under Title IX. If you have experienced any form of sexual harassment, sexual assault, domestic violence, dating violence, or stalking, know that you are not alone. The Title IX Office, the Campus Advocacy, Resources, and Education (CARE) office, and Counseling and Psychological Services (CAPS) are all resources that you can rely on for support.
Please be aware that if you tell me about a situation involving Title IX misconduct, I am required to share this information with the Title IX Coordinator. This reporting responsibility also applies to course TAs and tutors (as well to all UCSC employees who are not designated as "confidential employees", which is a special designation granted to counselors and CARE advocates). Although I have to make that notification, you will control how your case will be handled, including whether or not you wish to pursue a formal complaint. The goal is to make sure that you are aware of the range of options available to you and that you have access to the resources you need.
Confidential resources are available through CARE. Confidentiality means CARE advocates will not share any information with Title IX, the police, parents, or anyone else without explicit permission. CARE advocates are trained to support you in understanding your rights and options, accessing health and counseling services, providing academic and housing accommodations, helping with legal protective orders, and more. You can contact CARE at +1-831-502-2273 or care@ucsc.edu.
In addition to CARE, these resources are available to you:
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.
| work | total points available |
|---|---|
| final design reports | 400 |
| pre-lab drafts of design reports | |
| 10 in-class quizzes | |
| other homework | 35 |
Total points=~617628
| lowest points for grade | ||
|---|---|---|
| grade | from percentage | used |
| A | 589 | 570 |
| A- | 550 | 535 |
| B+ | 511 | 495 |
| B | 432 | 425 |
| B- | 393 | 383 |
| C+ | 354 | 350 |
| C | 275 | 270 |
| C- | 236 | 230 |
| D+ | 197 | 190 |
| D | 118 | 115 |
| D- | 79 | 75 |
The grading scale for each of the five design reports will be
| letter grade | points |
|---|---|
| A | 80 |
| A- | 74 |
| B+ | 66 |
| B | 60 |
| B- | 54 |
| C+ | 46 |
| C | 40 |
| C- | 34 |
| D+ | 26 |
| 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 in the schedule are tentative and may be changed.
The homework will be weighted approximately 1 point per question—the points given in the schedule are tentative and may be changed.
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 homework and pre-lab design work. (I haven't needed to do the large quizzes for several years.)
Because of the size of the class and the grading bandwidth, reports, quizzes, homework, and pre-lab drafts will not be accepted late and cannot be redone for credit.
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 (some of the questions are new each year).
The labs are contained in the textbook, rather than as separate lab handouts. The entire book (except for sections marked "optional" in the 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 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 the two quarters. Partnerships will be assigned randomly by the instructor and posted on Piazza. Zoom will be set up with breakout rooms corresponding to the partnerships, and Canvas will have the partnerships entered.
Each lab report will be done in two drafts: one due before the 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 your lab partner, by e-mail at least 8 hours (and preferably more) before the deadline, so that the group can be split. Otherwise only the last submitted report for the group will be graded.
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 your kits) are also required while soldering.
| Date | Lab |
|---|---|
| Mon 29 March 2021–Fri 2 April 2021 | Lab 7: Electret microphones |
| Mon 5 April 2021–Fri 9 April 2021 | Lab 8: Loudspeakers |
| Sat 10 April 2021 | Lab 7+8 report due |
| Mon 13 April 2021–Fri 24 April 2021 | Lab 9: Microphone preamp |
| Sat 25 April 2021 | Lab 9 report due |
| Mon 27 April 2021–Fri 30 April 2021 | Lab 10: FETs |
| Mon 3 May 2021– | Lab 11: Class-D power amp |
| Sat | Lab 10+11 report due |
| Lab 12: electrodes | |
| Sat 22 May 2021 | Lab 12 report due |
| Mon 24 May 2021–Fri 4 June 2021 | Lab 13: EKG |
| Wed 9 June 2021 | Lab 13 report due |
Homework, pre-lab reports, and lab reports will all be turned in as single PDF files through Canvas. The deadline will be 11:59 a.m. on the due date—that is in the morning. There is a 3-hour grace period (to 3 p.m. Pacific Time) for late submissions, but anything later than that will not be accepted. Submit before the deadline and use the grace period only for dealing with upload problems or wrong-file problems. On partner submissions, use the grace period to check that your partner has submitted a readable PDF file.
Quizzes will be open generally from 1 a.m. to 8:30 p.m. Pacific Time on Thursdays. They are timed, open-book, open-notes quizzes, with no internet or human help permitted. You may use programs on your own machine (like gnuplot) to help with calculations. You have to submit a single PDF file with the quiz answers before the quiz times out—practice using a scanner app (or however you will be creating your PDF files) before taking the first quiz.
This course is deliberately "front-loaded," with heavy reading and homework loads at the beginning of the quarter, but light loads in the last two weeks of the quarter (reversing the pattern of most other courses).
| Due | Read before class or lab | Turn in before noon (Pacific Time) |
|---|---|---|
| Mon March 29 | Chapter 26 (microphones), Lab 7 | |
| Tues March 30 | HW 1: 26.1–26.6. Pre-Lab 7.1–7.3 | |
| Wed March 31 | Chapter 28 (inductors), 29 (loudspeakers) | HW 2: 26.7, 26.9. |
| Thu April 1 | Pre-Lab 7.1–7.5; Quiz 1 | |
| Fri April 2 | Lab 8 (loudspeaker modeling) | HW 3: 28.1, 29.1–29.6 |
| Sat April 3 | Pre-Lab 8 | |
| Mon April 5 | ||
| Wed April 7 | Lab 9 (audio amp) | |
| Thu April 8 | Quiz 2 | |
| Fri April 9 | Chapter 32 (Field-effect transistors) | Pre-Lab 9 |
| Sat April 10 | Lab 7+8 report (microphones and loudspeakers) | |
| Mon April 12 | ||
| Wed April 14 | Chapter 33 (comparators) | |
| Thu April 15 | Quiz 3 | |
| Fri April 16 | Lab 10 (Measuring FETs) | HW 4: 32.1–32.3 |
| Mon April 19 | Sections 35.1–35.6 | |
| Wed April 21 | Sections 35.7–35.10 | |
| Thu April 22 | Quiz 4 | |
| Fri April 23 | HW 5: 35.1–35.6 | |
| Sat April 24 | Lab 9 report (preamp) | |
| Mon April 26 | Lab 11 (power amp) | |
| Wed April 28 | ||
| Thu April 29 | Quiz 5 | |
| Fri April 30 | ||
| Sat May 1 | Pre-Lab 11 (Class-D amplifier) | |
| Mon May 3 | Chapter 38 (Electrodes) | |
| Wed May 5 | Lab 12 (electrodes) | |
| Thu May 6 | Quiz 6 | |
| Fri May 7 | ||
| Sat May 8 | ||
| Mon May 10 | Chapter 40 (instrumentation amps) | HW 6: 38.1–38.3 |
| Wed May 12 | Pre-Lab 12 (electrodes) | |
| Thu May 13 | Quiz 7 | |
| Fri May 14 | ||
| Sat May 15 | Lab 10+11 report (FETs and Class D) | |
| Mon May 17 | Chapter 41 (EKGs) | HW 7: 40.1–40.3 |
| Wed May 19 | Lab 13 (EKG) | |
| Thu May 20 | Quiz 8 | |
| Fri May 21 | ||
| Sat May 22 | Pre-Lab 13 (EKG) | |
| Mon May 24 | Lab 12 report (electrodes) | |
| Wed May 26 | ||
| Thu May 27 | Quiz 9 | |
| Fri May 28 | ||
| Mon May 31 | Memorial Day, no class | |
| Tues June 1 | Redone lab reports (optional) | |
| Wed June 2 | ||
| Thu June 3 | Quiz 10 | |
| Fri June 4 | ||
| Wed June 9 | Final exam time: 12–3 p.m. probably not used. | Lab 13 report (EKG), final deadline for all work. |
|
|
| 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