(Last Update: 2018 March 6 16:43 PST )

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: Pallavi Karhade pkarhade@ucsc.edu
• Piazza forum for discussions: https://piazza.com/ucsc/winter2018/bme51a/home The Piazza page is the preferred way to ask questions (except for personal items like illness or disability accomodations).
• Class meetings: Thimann 1 12–1:05
• Lab meetings: Active Learning Classroom (Science and Engineering Library)
  TTh 5:20–6:55 (Section 1) Group tutors: Henry Hinton, Andy Baldovino
  TTh 7:10–8:45 (Section 2) Group tutors: William Van Hyning, Jason Prince
• Final exam time: Monday March 19 4–7 p.m. (may not be used)

Overview

The course is intended for sophomores and juniors in bioengineering 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)

Students considering the bioelectronics or assistive technology: motor concentrations should take BME 51A+B early (before EE 101/L), which may be difficult to schedule. Key for the motor concentration is getting CMPE 118 (Mechatronics) in fall of the junior year—scheduling should be designed to ensure that, even at the expense of non-optimal course ordering.

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.

The old bioengineering curriculum (before the 2014–15 catalog) will accept BME51A+B as fulfilling the EE101/L (circuits) requirement, but EE will not be accepting it as a prerequisite for further electronics courses. More recent curricula (starting 2014–15) for bioengineers requires BME 51A+B for all concentrations, and EE 101/L in addition for the bioelectronics and assistive technology: motor concentration.

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

• use a hand-held multimeter.
• solder through-hole parts.
• use USB-controlled oscilloscope, function generator, and power supply.
• Added 6 March 2018: install and use python, gnuplot, PteroDAQ data acquisition system, and Waveforms 2015 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.
• Added 6 March 2018: draw useful block diagrams for amplifier design.
• Added 6 March 2018: draw schematics using computer-aided design tools.
• write design reports using LaTeX.
• 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:

What to buy

Tools and Parts

This year the parts and tools are covered by the course lab fees. There are about $80 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.

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, or Linux.

The Analog Discovery 2 USB oscilloscope, function generator, and power supply that will be used in the labs is controlled by Waveforms 2015, which is freely downloadable from http://store.digilentinc.com/waveforms-2015-download-only/ 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 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 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.

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 useful for digital filtering of heartbeat signals. You can substitute the Enthought bundle, or use the Python.org site Python (either 2.7 or 3.4–3.6). 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.

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. You may use your own

Software written specifically for the course—all of which is free:

• download for data acquisition software PteroDAQ should work under Windows, Mac OS X, and Linux, with either Python 2.7 or Python 3.4 or newer. See https://bitbucket.org/abe_k/pterodaq/wiki/Home for more information, including installation instructions.
• definitions.gnuplotUseful definitions in a gnuplot script for Bode plots and impedance modeling
• Filter program for doing bandpass 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.

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 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 (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 plan to have a release of a new version of the book during December 2017, with substantial new content, bug fixes, and new exercises. I'll send out the coupons to those registered for the course as soon as I get the new version up.

I have been writing this book specifically for this class, and it is not quite done. If there is time, I will be rewriting or expanding portions of the book during the quarter, so you may need to download the PDF file again for 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://www.elecraft.com/TechNotes/N0SS_SolderNotes/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/FabLab#StandardOperatingProcedures

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 may assign some of these, but you are encouraged to try them on your own whether or not they are assigned.

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

If your understanding of complex numbers is rusty, and you get confused by our frequent use of them for talking about sine waves, then you might want to check out Wise Warthog's recommended 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.

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 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).

Added 2018 Feb 16. 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.

Added 2018 Feb 16. 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.

To do for next year: rearrange schedule to do 4 days of temperature measurement and 3 of sampling and aliasing.

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.

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, lab reports cannot be redone to get a higher grade—only those reports with a grade of "REDO" can be redone, and they must be redone, or they will be converted to "F". Redone reports have a new due date a week after the reports are returned to the class.

Grading standards are somewhat higher for redone reports, so that minor errors that would have been tolerated earlier will be judged more harshly in a redone report. All previously graded versions of the report must be turned in with any redone report.

Added 2018 Feb 16. Don't trust the Canvas summary of your grade. The Canvas gradebook seems to be incapable of averaging the grades correctly (in part because it has essentially no understanding of letter grades and very poor handling of ungraded or not yet due homework), so I will need to download the records from it and compute grades separately.

The grading standard for the design reports is not "point-based"&emdash;I'm not looking for specific items and taking of 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. Serious errors in the schematic may be enough by themselves to reduce the grade below passing.

Homework

Homework schedule is still somewhat tentative, due to 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.

Note to self: schedule still needs tweaking for better fit to new exercises and pre-labs. Check that all exercises have been assigned somewhere (or marked as not assigned). Don't assign any exercises from Chapter 14 (oscilloscopes).

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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