(Last Update: 2020 March 25 13:04 PDT )

Instructor and Assistant(s)

• Kevin Karplus Office: Physical Sciences Building 318, Office hours: Tues 10:30–11:30am, Fri 12:40–1:40 karplus@soe.ucsc.edu
• Teaching Assistant: None
• Piazza forum for discussions: https://piazza.com/ucsc/winter2020/bme51a The Piazza page is the preferred way to ask questions (except for personal items like illness or disability accommodations).
• Class meetings: PSB 114 MWF 4–5:05
• Lab meetings: Baskin Engineering 111 and 113
  TTh 3:20–4:55 (Section 1) Group tutors: Ali Fallahi afallahi@ucsc.edu, Todd Nabonne tnabonne@ucsc.edu
  TTh 5:20–6:55 (Section 2, Baskin 111 only) Group tutor: Chris Cheney crcheney@ucsc.edu
• Optional group tutoring sessions: Ali Fallahi is running group discussion sections in Baskin Engineering 111 (corner lab) Wednesdays 5:20–6:25 (right after lecture) and Fridays 1:20–2:25 (overlapping with office hours).
• Final exam time: Thursday, 19 March 2020 12&–3 p.m. (may not be used)
• Graders: Brian Naranjo, Samatha Braun, Grant Skidmore, Jonathan Nguyen, Charles Cai, Ali Fallahi

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 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. 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 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 and while using the drill press.

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 a.m. on the due date—that is in the morning.

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).

Overview

The course is intended for sophomores and juniors with priority given to bioengineering majors, but is open to anyone who meets the prerequisites:

• Calculus (Math 19A or AP Calculus BC with 4 or 5)
• high-school physics (or Physics 5C or 6C)

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 51A). 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/

Because there have been 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.

Learning outcomes

Students will be able to

• use simple hand tools (screwdriver, flush cutters, wire strippers, multimeter, micrometer, … ).
• solder through-hole parts.
• use USB-controlled oscilloscope, function generator, and power supply.
• install and use python, gnuplot, PteroDAQ data acquisition system, and Waveforms 3 on own computer.
• predict the effects of discrete-time sampling on the representation of a signal.
• do simple optimizations (setting derivative to 0).
• do computations involving impedance using complex numbers.
• use hysteresis to reduce the effect of noise on digital interpretation of a signal.
• design single-stage high-pass and low-pass RC filters.
• design, build, and debug simple op-amp-based amplifiers.
• draw useful block diagrams for amplifier design.
• 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 51A 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 mandatory 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/winter2020/bme51a.

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.

Ali Fallahi is running group tutoring sections in Baskin Engineering 111 (corner lab) Wednesdays 5:20–6:25 (right after lecture) and Fridays 1:20–2:25 (overlapping with office hours).

What to buy

Tools and Parts

This year the parts and tools are covered by the course lab fees. There are about $70 worth of tools, parts, microcontroller board, and USB cable. These tools and 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 tools and parts.

The parts list for the quarter can be found at https://gasstationwithoutpumps.wordpress.com/parts-and-tools-list-for-bme-51a-winter-2020/

Textbooks

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 will be given a coupon for a free electronic copy of the textbook, 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 (28.7 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 released of a new version of the book on 2019 December 9, with substantial new content, bug fixes, and some new exercises. I sent out coupons for free PDF copies of the book to everyone registered for the class then. Anyone who registered later needs to email me.

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. (Students will be paid at the end of BME 51B.)

Soldering instructions

https://learn.sparkfun.com/tutorials/how-to-solder---through-hole-soldering
http://www.instructables.com/id/How-to-Solder-Videos%3A-Why-is-soldering-difficult-s/
http://radiojove.gsfc.nasa.gov/telescope/soldering.htm
http://ftp.elecraft.com/TechNotes/N0SS_SolderNotesV6.pdf

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 SOP before you are allowed to solder. Standard Operating Procedure (SOP) from the UCSC Baskin Engineering Lab Support (BELS)

Drill-press Standard Operation Procedures

https://bels.soe.ucsc.edu/sites/default/files/SOP_DrillPress_2016_RevA_02DRAFT.pdf

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 won't assign these, but you are encouraged to try them on your own if you need more practice.

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

The Art of Problem Solving Alcumus site has very good algebra tutorials (including complex arithmetic) if you need review.

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.

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. 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.

The Analog Discovery 2 hardware will be available in the lab, but Baskin Engineering Laboratory Support (BELS) will have a few that students can rent for the quarter. Contact the BELS staff directly for more information.

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.

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 substitute the Enthought bundle, or 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 an 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. 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:

• Data acquisition software: https://github.com/karplus/PteroDAQ PteroDAQ should work under Windows, Mac OS X, and Linux, with either Python 2.7 or Python 3.4 or newer. The README file on github has a pointer to the installation instructions.
• 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.

Laptop Policy

You should bring your laptop to every lab. It will need to have at least one and preferably 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.

You may bring your laptop to lecture to take notes, look up things in the book, try out examples of gnuplot or LaTeX, or other activities directly related to the class. If you do something else (check e-mail, browse on the web, read Reddit, &ellip; ), please sit in the back row, so that your screen will not distract others in the class.

Recording Policy

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.

Academic Integrity

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.

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.

Total points=658

Thresholds:

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 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.

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 homework and 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 (some of the questions are new this year).

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.

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 +1-831-459-2089, 459-4806 (TTY), or by email at drc@ucsc.edu.

Title IX and CARE

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:

• If you need help figuring out what resources you or someone else might need, visit the Sexual Violence Prevention and Response (SAFE) website, which provides information and resources for different situations.
• Counseling and Psychological Services (CAPS) can provide confidential counseling support. Call them at +1-831-459-2628.
• You can also report gender discrimination and sexual harassment and violence directly to the Title IX Office, by calling +1-831-459-2462 or by using their online reporting tool.
• Reports to law enforcement can be made to the UC Police Department, +1-831-459-2231 ext. 1.
• For emergencies, call 911.



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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