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BioE 10 - Introduction to Biomedicine for Engineers - 2021 syllabus
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BioE 10: Introduction to Biomedicine for Engineers

Department of Bioengineering, UC Berkeley


“Many technological systems, when examined for context and overall design, are basically anti-people. People are seen as sources of problems while technology is seen as a source of solutions.” - Ursula Franklin

Course Format:

Lecture slides:

Important notes:

Instructor: Terry Johnson

GSIs:

Office Hours:

Course Description

This course is designed to introduce undergraduates to the types of problems that bioengineers solve and the concepts they apply to solve them. Various types of devices - from genetically engineered bacteria to biosensors - will be discussed, and we will explore the physics and biology necessary to understand and design each of these devices. In addition, students will learn how to work effectively in groups and to communicate their results in a professional manner.

While this syllabus is meant to be an accurate description of the course and its content, it may be modified at the instructor’s discretion.

Objectives

To introduce students to the field of bioengineering and, in general, to thinking about problems and solutions in the field ethically and effectively.

Grading Policy

There are a variety of assignments for the course available on bCourses, where you can find their point values and due dates. Most of these assignments are due at the end of the month, so that they can be engaged in flexibly. Students are strongly encouraged to work ahead when possible, because they will receive no credit for late work. Last minute extensions, barring extraordinary circumstances, will not be granted. If there is a power outage or similar situation, all due dates will be pushed back, and details will be communicated via bCourses announcement.

There are a total of 300 points that can be earned in BioE 10. The final grading is not curved, and the breakdown is as follows.

Grade

Score

A

270

A-

260

B+

250

B

240

B-

230

C+

220

C

210

C- / P

200

D+

190

D

180

D-

170

We expect you to work with others in this class. While copying on individual assignments is not allowed, collaboration on these assignments is very much encouraged. You will be assigned a project group and they - or another group of students in the class - should be a regular part of your week as you work together to understand the material and complete assignments.

There will also be assignments that are turned in as a group. The instructor reserves the right to assign different grades to various members of the group, or to remove a member from a group to work on an ad hoc individual assignment, if the workload on a group assignment is not distributed and carried out evenly. Students who are taking the class on a Pass/Fail basis should take special note of this policy.

Assignments fall into a few different categories:

This model gives you more authority over your workflow than weekly assignments do, but with that comes the responsibility to keep up with the material. If you wait until the last week to attempt to complete a month’s worth of work, and find it difficult to get all the help that you need in the time remaining, that’s on you.

Be aware of UC Berkeley's Code of Student Conduct. Plagiarism or cheating will not be tolerated, and will result, at minimum, in a zero for the assignment. Plagiarism includes appropriation of whole passages with or without credit, appropriation of words and phrases without credit, appropriation of both main and supporting ideas without credit, and paraphrasing without credit. Plagiarism also includes submitting a paper written by someone else.

Regrade policy

If you would like to contest a grade, you must send an email to Amanda Meriwether with [BioE 10 REGRADE] as the subject line, briefly describing the issue within 1 week of the grade being posted. You should not expect that the instructor or the GSI will regrade anything while in conversation with you - that would not be fair to the other students in the class, whose homeworks have been graded without them present. Regrade requests should be based on an error on our part (e.g., adding up the points incorrectly) or what you suspect is a misunderstanding of your work (e.g., arriving at the correct answer using an unexpected technique). Regrade requests that argue with the rubric (e.g., “this is wrong, but you took too many points off”) will not be considered.

Your homeworks should stand alone. If a homework is disorganized or ambiguous, and requires an extensive explanation to the grader, you will likely still lose points.

Asking for help

Dealing with unavoidable circumstances is part of my job. If something is preventing you from a satisfactory engagement with this course, consult the Academic Accommodations Hub to determine if there is a campus resource that can guide you. If there is, the instructors will work together with that resource to accommodate you. If not, or if you are unsure , please contact the instructor directly.

Course Content

Introduction

Reading:

References:

Device 1 - Genetically engineered yeast

Theory: Molecular biology; genetic engineering

Practice: Intellectual Property

Reading: Production of the antimalarial drug precursor artemisinic acid in engineered yeast

Reference (not required): Primer for synthetic biology - part 1

Device 2 - DermaGraft

Theory: Physiology; biomaterials

Practice: Regulatory concerns; hypothesis testing

Readings:

References (not required):

Device 3 - Home pregnancy test

Theory: Immunochemistry, Fluid dynamics

Practice: Identifying needs and solutions

Reading:

References:

Device 4 - Electrocardiograph

Theory: Signals

Practice: Street-fighting mathematics

Readings:

Final Project

Each group of five students will be jointly responsible for the final product as a whole, and though you may split the work up amongst yourselves, all of you will be expected to comprehend and be able to explain any part of the final product.

If any member of the group is unable to do their share of the work due to unforeseen and extraordinary circumstances, it is that student’s responsibility to inform the instructor as soon as possible so that alternate arrangements can be made. The instructor reserves the right to assign different grades to various members of the group, or to assign alternative individual projects, if the workload is not distributed and carried out fairly. Students who are taking the class on a Pass/Fail basis should take special note of this policy.

There is a required format for your final paper. If all of this formatting stuff below seems picky, the goal is to make the grading as fair as possible. I want everyone’s paper to look the same so our brains are evaluating the content, not being unconsciously affected by the layout or font choice.

The final project consists of a six page maximum (not including Works Cited, Appendix I, II, and the project contract) paper. This paper should be in a 2-column format consistent with IEEE submissions (Times New Roman, font size 10 for main text, 14 for the title, 12 for subheadings, single spaced, 1 inch top/bottom margins, 0.7 inch left/right margins). Please note that larger charts, diagrams, tables, etc. should break from the 2-column format and take the entire width of the page. All tables and figures should be numbered and have a descriptive legend.

I. Introduction - A description of the device, its function, and its operating principles. A brief history of the device’s development. Finally, a description of the problem that the device solves. Some devices may be applied to more than one problem; if so, choose one and focus on it. Typically 1 - 1.5 pages.

II. Alternatives - A list of alternate solutions, including a weighted selection matrix. It is perfectly acceptable to conclude that your device is not the best device!

III. Key Challenges - This should include a focus on at least one other practical concern (efficacy testing, the regulatory process, etc.) discussed in the course.

IV. Ethical Issues - Consider at least one ethical issue associated with your device. This issue could be associated, for example, with the construction, application, or economics of your device. Typically 0.5 - 1 pages.

V. Conclusions - Indicate what you think the best solution(s) to the problem are. If your device or any of your solutions are speculative (e.g., not yet available), indicate which of the available options is best, and also which of all of the devices you expect would be best, were all to become available. Discuss aspects of your analysis that you find troubling or inconclusive. Typically 0.5 - 0.75 pages.

The Works Cited below should be in the same formatting as the above, but does not count towards the 6-page maximum.

Works Cited - your citations should consist primarily (though not necessarily exclusively) of peer reviewed journal articles. If you aren’t sure if something is a peer reviewed journal - ask! Citations from the peer reviewed literature usually have a DOI number. Citations should be in the IEEE format.

The appendices and project contract do not count towards the 6 page maximum, and they may be formatted however the team chooses, so long as it is readable.

Appendix I - minutes from weekly group meetings. These should include: the date and time of each meeting, a list of participants, the agenda, minutes (brief notes of what was discussed), and the action items generated.

Appendix II - a copy of the personal goals statement for each team member detailing what that student wants to get out of the project experience along with a brief (250 words or fewer) statement from each team member discussing what steps that member took during the project to meet those goals.

A signed project contract

A sample LaTeX template (on bCourses) and Google doc template are available for you, though you may use another document editor (e.g., Microsoft Word) to produce your document if you wish. If you decide to go with LaTeX, there are many free options available. I have TeXworks installed as an editor with TeXLive on my laptop, and if you’d prefer to work collaboratively online, OverLeaf is an editor that you can use directly in a browser.