BME 88A W16
BMES Freshman Design Seminar

(Last Update: 2016 March 18 16:14 PDT )

Overview
Blog
Accommodations for disability
Academic Integrity
Homework
Schedule

Overview

This freshman design seminar is a limited to first-year students (second-year allowed in if there is room) who are proposed bioengineering majors. Class size is limited due to limited lab capacity.

This is a first course in engineering design for bioengineers. Students choose a design project and work on it in cooperative teams. Covers team building, design, prototyping, and report writing.

Instructor:

Kevin Karplus karplus@soe.ucsc.edu

Office hours:

PSB 318, W 4–5, Th 2–3

Meeting times:

MWF 2–3:10, Physical Science Building 305
We'll sometimes meet in the EE circuits lab (Baskin Engineering 150).

Group Tutor:

None hired yet

E-mail discussion

There is an e-mail discussion group for the class. All students in the class should participate in e-mail discussions. Other people may request joining the discussion, to be allowed in or not at the discretion of the class.

Overview:

This course is a 2-unit freshman design seminar, first offered as a prototype in Winter 2014 (as BME 94F), and it is still under active development. Students will be helping design the course, as well whatever design projects we take on.

The current goal for the design projects is to have small teams (2–3 students) design low-cost lab equipment suitable for hobbyists or home school, middle school, or high school science labs. Think of it as "science on a shoestring" or "thrift-store science". We'll be trying to duplicate the functionality of expensive science teaching tools (such as those sold by Pasco and Vernier) at a fraction of the price. But the course is driven by what the students want to learn and do—if you have an idea for a project, bring it up in class.

A major goal of the course is to get students thinking like engineers: asking questions like "How can we make something that does this?", "What are the constraints on the design?", "Will this part do what we want?", "How much would it cost to do that?"

Another goal of the class is to get students to learn on their own to meet their own needs for knowledge, rather than relying on teachers to tell them what to learn. Initially, you'll be directed to look for certain information, to develop your skills at finding and evaluating information—later you'll be asking your own questions that need answers.

Target audience:

The primary audience are freshman bioengineering proposed majors. If space permits, we may allow in a few 2nd-year or transfer students. Seniors interested in the course are encouraged to attend the first day and apply to be group tutors.

Prerequisites:

This is intended for first-year students, so there are no prerequisites. Students should come in with an interest in designing and constructing things. Prior experience with hand tools, soldering, computer programming, and so forth are all valuable, but no specific skills are required to join the class.

Requirements satisfied:

This course does not satisfy any bioengineering graduation requirements, nor is it a prerequisite for any further courses. It does provide a PR-E (Collaborative endeavor) general-education code.

Take this course because you want to do it, not because you have to. Because it does not satisfy any BSoE major requirements, it is reasonable to take the course P/NP, instead of for a grade. Expect to average about 6 hours/week on the course, perhaps a bit more if your group gets excited about their project.

Evaluation:

Students will be evaluated on the written, oral, or poster presentations of their designs, as well as on how well their prototypes meet the design goals they set. It is not necessary for a prototype to work to pass the course, as long as good attempt has been made at doing the design and debugging it, and that attempt has been properly documented.

Constraints on the course:

The main constraints on the course are that it is 2 units, so should average only 6 hours a week, and that it has "Practice: Collaborative Endeavor" general-education credit, so must involve learning how to do group work effectively.

Blog

There is some discussion of the goals of the course and ideas for possible projects on Prof. Karplus's blog http://gasstationwithoutpumps.wordpress.com/freshman-design-table-of-contents/

Please feel free to leave comments on the blog with suggestions for the course.

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 me during my office hours in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY).

Academic Integrity

Anyone caught cheating in the class will be reported to their college provost (see UCSC policy on academic integrity) 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 all assignments with explicit written acknowledgment is encouraged—guidelines for the extent of reasonable collaboration will be given in class.

Homework

• Intake survey Do in class Mon, 2016 Jan 4.
• By Wed. 2016 Jan 6. Start keeping a log of time spent on this class. You should be spending 6 hours a week on a 2-unit course: 3.5 hours in class and 2.5 hours outside class. Keep your log of minutes spent in a spreadsheet format, with each day on a different row. Columns should be something like "date", "class time", "reading", "design work", "programming", "writing". Come up with headings that make sense to you—two ideas that came up during class were adding "construction" or "prototyping" and splitting each column into expected and actual times.

  I'll want to see the logs weekly, so that I can adjust assignments to avoid overworking students. Perhaps the simplest thing to do is to keep the log as a Google spreadsheet and give me (karplus@soe.ucsc.edu) read access to the spreadsheet—make sure the spreadsheet has your name on it, so I can keep them straight, as Google provides only non-mnemonic names for files.

  We'll look at different student spreadsheet designs in class, to take good ideas from each other.

• Turn in by e-mail by midnight Friday, 2016 Jan 8: Look on-line for projects that might be interesting to design or build this quarter. Look at sites like Pasco, Vernier, and Arbor Scientific for ideas about what schools with money have in their labs. Look for do-it-yourself lab equipment ideas on the web. Turn in an annotated list of URLs for interesting sites as plain text, cut-and-pasted into e-mail to karplus@soe.ucsc.edu. Even better, mail to the whole class at bme88a-w16@soe.ucsc.edu. The annotation need not be extensive—a sentence about each web site, telling us what project(s) it has information about, should suffice. Raw URLs without annotation, however, are not acceptable. You should also explore whether the full URL is needed to get to the site—a lot of web sites add all sorts of extra tracking or status junk to URLs, and it is good practice to strip the URLs down to the essentials.
• Before class Wed 2016 Jan 20, install Arduino IDE and Teensyduino add-on on your own computer (Mac, Linux, and Windows should all work). Write and test a program that blinks the on-board LED (pin 13).
• DUE Saturday, 2016 Jan 23, midnight.

  Your next assignment is to pick projects from two other students and research them further, looking for more information, other design choices for the same result, possible problems with doing the design, workarounds for the problems, and so forth.

  For each project you research, you should send an email to the class mailing list (bme88a-w16@soe.ucsc.edu), sharing what you have found and thought about. Discuss only one project in each email, and use BME88A and the project name (PCR machine, UV sensor, photogate, incubator, pulse monitor, ...) as the subject line of the message, so that others can find the messages about particular projects more easily. Respond to each other's research—if some one has identified a possible problem, and you've got an idea how to solve that problem or have found a resource on the web that addresses it, reply to everyone to contribute to the discussion!

  I am expecting at least two email messages (two different projects) on the email list from each of you—sooner is better, so that everyone can read and think about your ideas before Monday's class. I hope that we can then discuss the projects that students found most interesting in class, with several people having already looked at the projects in some detail.

• Due Monday, 2016 Feb 1. Design a colorimeter for measuring OD600 in the Brand cuvettes you got in class. I've bought LEDs, (student choice of LTL-4273 and 333-2UYC/H3/S400-A6) phototransistors (LTR-4206), and foamcore.

  I want you to design a colorimeter for measuring OD600 in the cuvettes you got. (Keyword=optical density) (also look up what OD600 is used for in monitoring cultures)

  Design the mechanical part of the colorimeter so that the light source and photosensor are on opposite sides of the cuvette in a straight line perpendicular to the faces of the cuvette and there is no ambient light on the photosensor.

  You might want to get yourself a razor knife (Exacto knife or cheaper equivalent) for cutting and scoring foam core (I have a few, but not enough to provide one for everyone).

  I want each pair to build a prototype colorimeter that can measure the light coming through a cuvette. Your design needs to

  • hold the LED and phototransistor in alignment,
  • keep the cuvette from rotating (the faces of the cuvette should be at right angles to the light path),
  • keep ambient light from reaching the phototransistor, and
  • measure and report the light reaching the phototransistor.
  You should bring the finished prototype to class on Monday.

  Optional bonus assignment (programming): have the program record the light through a cuvette filled with water, and use that as reference to compute absorbance:
  log_10 ( light with just water / light with absorbing material)

  For sizing the resistor on the phototransistor, you'll need to know how much current to expect—see https://gasstationwithoutpumps.wordpress.com/2016/01/26/phototransistor-i-vs-v-plots/ for a plot of the current vs. voltage that I measured for the phototransistor, illuminated by one of the LEDs.

  Be prepared on Friday 2016 Jan 29 to ask for the resistor(s) you need for your design.

• Turn in Mon 2016 Feb 8: Design report for a colorimeter (one report from each pair of students). A design report starts with a clear specification of the design goals: what does the device do? what constraints (cost, size, power available, and so forth) are there? The report continues with how you met the design goals, what problems arose, and how the problems were solved. There should be schematics for all electronics, complete with component values. There should be explanations (often computations) for how component values were chosen. There should be drawings, photographs, or both, sufficient for someone else to duplicate the physical design. Any external sources used should be clearly cited. As with all engineering documents, the authors' names and the date of the last revision should be on the first page, and all pages should be numbered. If you have any questions, please e-mail the bme88a-w16@soe.ucsc.edu mailing list, so that I can respond where everyone can read the answer.
• Turn in Mon 2016 Feb 22: Design proposal (one per group), containing at least the following:
  • Design specifications: what exactly are you designing? what does it do? How can I tell whether or not you've designed what you intended?
  • Block diagram: what are the subsystems of your design? How are they connected? What are the specifications for the interfaces?
  • Design problems: what resources, parts, tools, educations, ... do you need to design and make for your block diagram to work?
  This design proposal is a first draft of the final report, and you will keep adding to it for the rest of the quarter.

  Also, by that date you should have ordered all the parts you need.

• Turn in Mon 2016 Feb 29: More detailed design report (one per group). Fill in the incomplete design specs from last time. Have a block diagram showing all the functional subsystems, including both hardware and software. Try to have a complete schematic for the hardware so that you can order parts (before Feb 29) and ask questions about parts of the design that you are struggling with.
• Turn in Mon 2016 March 7: More detailed design report (one per group). Have block diagrams showing all the functional subsystems, including both hardware and software. Have a complete schematic for the hardware so that you can debug (note: the LED cube projects can use some "…" to show repetition, but pin numbering on chips needs to be clear).

  Some of the software needs to be written—include it as an appendix to the report.

  In this draft of the final report, indicate any changes to the design, progress on building the prototype, difficulties you need help resolving, and so forth.

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The homework listed below here is based on the Winter 2015 offering of the course. I expect the homework to be different this year, as what students need to learn will depend on what the students in the class want to pursue as projects. The web page will be updated as the class progresses.

Note: due dates below here are probably too late for completion of projects. We'll try to get projects started earlier this year.

• Turn in ?: Work individually and show derivations for formulas (based on Ohm's law):
  1. What is output voltage of voltage divider if the two inputs are connected to V_A and V_B instead of to V_in and GND? (Given: no current through the output port.)

     The following circuit may not be identically labeled to the one I showed in class. I've also used batteries and a voltmeter here to make it clearer exactly what voltages we are talking about.

     
  2. What is the formula for the output of a negative-feedback op amp circuit? (Given: no current through the inputs of the op amp, and negative feedback holds the two inputs of the op amp to the same voltage.)

     Here is the circuit I gave in class. The labeling may be different from what I drew on the board, since this is an old version of the schematic that I happened to have in Scheme-It:

     

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SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

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