Independent Study and Capstone Options for BMEB Majors

Doing research as an undergrad

One of the main advantages of being a student at the University of California is that the faculty are actively engaged in cutting-edge research. You gain most from this if you get involved in the research yourself — research experience is one of the best ways to improve your chances of getting into grad school or getting a good job.

Biomolecular engineering students interested in wet-lab research should get involved early (end of second year), as wet-lab work is slow to provide results and the training is often quite lab-specific. Wet-lab faculty prefer students remain in the lab long enough to be productive researchers, which generally means at least two years. A two-year timeline means that one of the first tasks for transfer students in biomolecular engineering is to find and join a research lab.

Bioinformatics students are encouraged to get involved in research labs near the beginning of their senior year, after they have had substantial training in programming, though it is possible get involved much earlier.

Finding and joining a lab

Finding a lab doing interesting work requires some effort on your part, but we provide several tools to make this easier:

  • Websites: most of the research groups maintain active web pages outlining their main topics of interest and provide links to recent papers. If something looks interesting, try reading some of the papers, then email the principal investigator (PI) of the lab asking to discuss the papers during office hours.
     
  • Seminars: the BME department has weekly research seminars on Thursdays  11:40 a.m. – 1:15 p.m. During Fall quarter these talks are dedicated to showcasing labs that are interested in adding new researchers (usually grad students, but also undergrads). The seminar is listed as a grad class (BME 280B), but the talks are open to the public, so there is no need to sign up for the course.

    Seminars in other departments are also worth attending when there is a topic that looks interesting, as many BMEB majors conduct research with faculty from other departments.

     
  • BME 55: In Spring 2021, we prototyped a new 2-unit course for 2nd-year students to sit in on lab group meetings, read papers from the lab group, and report back to the other students about the results. The course allows students to make initial contact with labs and find out how lab groups work. The course will be offered again in Spring 2022 (and probably subsequent years).

If you are interested in a lab, ask questions about papers from the lab (showing you are interested in their work, and not just "looking for a lab") and ask if you can sit in on lab group meetings. Sitting in on a meeting fairly quickly results in determining your fitness for joining the lab. After attending meetings for a few weeks, you can start volunteering and asking about research projects you can contribute to.

Registering for independent study

Biomolecular Engineering and Bioinformatics (BMEB) majors are encouraged to work on group or individual projects doing scientific research or engineering design throughout their time at UCSC, and all students are required to do a capstone project.

There are several course numbers set up for organizing independent study and capstone work. Some of the courses are five units, which require 15 hours of work a week for 10–11 weeks (150–165 hours total), while others are two units (6 hours a week, or 60–66 hours total).

All five-unit independent study courses are require to have a written report at the end of each quarter, to be evaluated by the faculty member supervising the independent study. All two-unit independent study courses have an end-of-quarter report for evaluation by the faculty member — often one-on-one verbal reports from the student are acceptable.

"Faculty members" include not only Academic Senate faculty, but also lecturers and some senior research staff.

Register for independent study courses

  1. Meet with a faculty member who will be supervising the course and agree on a plan of work.
  2. Fill out an independent-study form (available from the Baskin Engineering Advising Office). Included on this form is a due date for end-of-quarter report (usually the first day of exam week). Discuss with the faculty supervisor and get their signature.
  3. Get the form signed by the undergraduate director, or have the undergraduate director email their approval to the advising office. This is generally a very quick check, as independent studies are routine for bioengineering majors.
  4. Drop off the form at the  Advising Office, where you will be issued the numeric codes needed for registering for the course.

Note: for thesis research (BME 195), you need to have a thesis proposal (a page or two) approved by the undergraduate director before your first registration for BME 195. This is not a rubber-stamp approval, and it often takes a couple of iterations to get an acceptable thesis proposal, so the process should be done before the first quarter of the thesis starts.

Independent study course numbers and what they mean

There are many different independent-study course numbers, with subtly different meanings. There are two types: a five-unit course, for which 15 hours a week of work is expected (150–165 hours total) and a two-unit course, for which six hours a week of work is expected (60–66 hours total).

It is also possible for students to work in a research lab without getting academic credit (a particularly common choice for the summer, to avoid paying extra tuition). When students are not getting credit, the amount of work expected and any reporting requirements are matters for negotiation between the faculty member and the student, not set by program policy.

BME 94 (5 units) and 94F (2 units): Group tutorial

These course numbers are intended for groups of lower-division (freshman or sophomore) students working together being supervised by a faculty member. They are also used for prototyping new lower-division courses, before the courses get approval by the Academic Senate's Committee on Courses of Instruction.

BME 99 (5 units) and 99F (2 units): Tutorial

These course numbers are intended for individual lower-division students being supervised by a faculty member.

BME 193 (5 units) and 193F (2 units): Field Study

These course numbers are intended for students doing work that is not on campus. Quite often this work is supervised primarily by someone who is not a UCSC faculty member, but a UCSC faculty member is needed to evaluate the work and file the grades.

BME 194 (5 units) and 194F (2 units): Group Tutorial

These course numbers are intended for groups of upper-division (junior or senior) students working together being supervised by a faculty member for projects that are not covered by capstone courses. They are also used for prototyping new upper-division courses, before the courses get approval by the Academic Senate's Committee on Courses of Instruction.

BME 195 (5 units) and 195F (2 units): Senior Thesis Research

These course numbers are intended for senior thesis research, one of the capstone options. A senior thesis requires 12 units of BME 195 (or 195F), plus five units of BME 123T, the senior thesis writing course. Each quarter of BME 195 should result in a draft of the thesis, to be evaluated and given feedback on by the faculty member supervising the thesis. BME 123T is normally taken in the middle of the senior thesis (Winter quarter), to work specifically on polishing the writing — there should already be a substantially complete first draft (except results) before BME 123T starts.

Completing the senior thesis capstone requirement requires passing 12 units of Senior Thesis Research, passing BME 123T, and submitting the thesis in PDF format as part of the senior portfolio.

BME 198 (five units) and 198F (two units): Individual Study and Research

These course numbers are intended for individual upper-division (junior or senior) students being supervised by a faculty member for projects that are not covered by capstone courses or senior theses. It is very common for a student to sign up for a two-unit 198F course when first joining a lab, to try out the "fit" with only a six-hour weekly commitment, not a 15-hour one.

Capstone Options

Biomolecular Engineering students have four capstone options:

  • senior thesis,
  • iGEM synthetic biology project,
  • group capstone project, or
  • the bioinformatics graduate classes used as the bioinformatics capstone.

Students in the bioinformatics concentration must take the bioinformatics graduate courses as their capstone.

Senior Thesis

A senior thesis is a single-author written document that provides a detailed description of about a year's intensive research by the individual research. It is not appropriate for team projects, which are handled through the other capstone options.

The senior thesis is highly recommended for students who plan to continue on to Ph.D. programs in graduate school, as the senior thesis is deliberately structured like a miniature version of a Ph.D. thesis, and so provides excellent training for graduate school. The thesis option also provides the most intensive writing practice and training of the capstone options, which is also particularly valuable for those continuing to graduate school.

The senior-thesis option is available in all concentrations, and the faculty adviser can be any faculty member at UCSC who has relevant expertise. The adviser can even be outside UCSC (in which case students register for BME 193 instead of BME 195), as long as there is a UCSC faculty member willing to review the work and issue grades as the instructor of record. Students need to turn in a statement from the outside supervisor permitting the project to be done (we've had some senior project cancelled by companies over IP disputes) and should turn in a resume or other detailed description of the outside supervisor with the thesis proposal.

Many of the senior theses are funded by grants managed by the faculty adviser, but this is not an essential feature of the thesis — a faculty member may agree to supervise a project without agreeing to fund it. Be sure you are clear on the source of funding for your research before committing to a thesis project.

Thesis Proposal

Before starting a senior thesis a one- or two-page thesis proposal is required. Send the proposal to the undergraduate director (dbernick@soe.ucsc.edu) as a plain-text or PDF file.

This proposal is essentially a first draft of the introduction to the thesis, starting with a research question or design goal, an explanation for why it is worth doing, and what experiments or prototypes will be done to answer the question or achieve the design goal.

The question or goal is for this specific thesis and must be reasonably completable in a year — it cannot be a vague description of research field nor a life work. It is not the goal of the lab where the research will be done, but the goal for this one-person project. The goal needs to be very clear and specific, so that someone reading the final thesis can tell whether or not the goal was met or the question answered.

The thesis proposal should also include who the faculty supervisor is, and confirm they have read and approved the thesis proposal.

The undergraduate director will be looking for a clear statement of the goal of the thesis in the first paragraph of the proposal, and preferably in the first sentence. If the first paragraph is just background or vague descriptions of the topic, the proposal will be need to be rewritten.

Thesis Expectations

A senior thesis is a single-author work whose main goal is to establish that the author is capable of carrying out a substantial research project. As such, it should be written in the first-person singular, past tense ("I extracted DNA with the following protocol … ") not passive voice and not plural, unless specific other participants are identified ("Postdoc X and I").

The audience for a thesis is not the faculty adviser nor the other members of the research group. In many cases they know more about the subject than the author, so writing for them is an exercise in frustration. Instead, the proper audience to write for is bioengineering majors who might join the lab to continue the project. Basic knowledge from lower-division courses can be assumed, but details of the particular problems and protocols of the lab need to be spelled out in the thesis.

The main body of the thesis has several parts:

  • An introduction, which sets out the research question (for a science thesis) or design goal (for an engineering thesis) and explains why the goal is interesting or important, and how the work done for the thesis answers the question or achieves the design goal. This introductory chapter is essentially a more fleshed-out version of the thesis proposal required before the thesis research is started.

    Don't bury the lead! The first paragraph of the thesis or thesis proposal should include the research question or design goal — subsequent paragraphs can expand on and clarify the initial question.

  • Background chapter or chapters explaining what has been done by others previously on the topic, including explanations of the major lab techniques that will be used. This chapter should have multiple citations from the primary literature in the field.
     
  • Chapters on the lab or design work actually done for the thesis, including what went wrong and how the problems that arose were addressed. Because the point of a thesis is to show that the student is capable of research, include descriptions of the debugging process used, not just the final results that "worked". This level of detail is quite different from a journal paper, where space limitations require cutting out all the dead ends.
  • The research chapters should be logically organized with experimental methods, results, and discussion of the results placed close together. In most theses, results from one experiment drive the choice of which other experiments to do, so it is important to describe and interpret the results as you go, not leaving that to a later section. (Note: some journal styles in biology call for separating methods, results, and discussion, under the general assumption that the methods consist only of routine procedures whose description would interfere with understanding the results of the experiments — that is a very different style than what is called for in a thesis.)

  • A concluding chapter summarizing the results of the thesis and describing what needs to be done next (either to finish answering the original question or to answer new questions that came up as a result of doing the research.)
     
  • An optional appendix containing detailed information that may be useful to some readers of the thesis, but which would interfere with the flow of information in the main body. This can include lab protocols, software, additional data that was collected, and other supplementary information.

Each quarter of BME 195 should end with the student turning in a complete draft of the thesis to the research adviser. In the first quarter, this draft should contain a complete introduction and background, and a research plan detailing what needs to be done to complete the thesis. At the end of the second quarter, the thesis draft should be well polished and nearly complete, with only a few results to be added from the final quarter of work (and any interpretation of those results).

Students doing a senior thesis are required to take BME 123T, a five-unit intensive writing course, which is intended to help students polish their writing. BME 123T is offered in winter quarters, which coincides with the second quarter of the thesis research for most students. Students must have a first draft of the thesis at the beginning of BME 123T, as the goal of the course is to edit the thesis and improve the writing while the project is on-going, not to create a first draft nor to polish the thesis after the research is completed.

iGEM Synthetic Biology Project

The group project in synthetic biology is a capstone intended for the biomolecular concentration, as it involves manipulating cells to do something that they do not normally do. The goal is usually to produce a substance or behavior in unicellular organisms that is not native to the organism. The overall goal may be highly ambitious (such as producing butanol as a fuel from digestion of cellulose), but the project for a single year needs to be realistically attainable in one summer of intense work (such as introducing one or two steps of the butanol-synthesis pathway into a bacteria strain).

Students join the iGEM team by joining the iGEM journal club in Fall, then signing up for BME 180 (2 units) in Winter quarter and BME 188A–C (5 units each) in Spring and Summer quarters. Interviews to join the team are generally held at the end of Fall quarter and the beginning of Winter quarter, and students have to show they will be productive members of the team during BME 180 in order to continue.

The synthetic biology project is available only on a spring and summer schedule, because it is synchronized with the international iGEM competition, which has their main event to present results at the end of September.

An important part of the synthetic biology project is learning how to fund projects — students are taught how to request funds from various internal University sources and how to do crowd-funding. The bulk of the funding for the projects comes from crowd-funding.

BME 129A–C Group Capstone Project

The BME 129A–C capstone is a mixture of group projects that don't fall into any of the preceding categories. As with the iGEM and thesis options, students are expected to write formal written reports of their projects.

Students are also responsible for finding funding for their group capstone projects, though very rarely some projects suggested by faculty will have funding available.

Bioinformatics Capstone

The bioinformatics capstone consists of a series of programming-intensive graduate courses. Although these courses are open to students in the biomolecular concentration, they have additional prerequisites that are part of the bioinformatics concentration, but not normally required for the biomolecular concentration.

CSE/ECE 129A–C Group Capstone Project

Many CSE and ECE group capstone projects are suitable for bioengineering students with concentrations in bioelectronics and assistive technology: motor, though the students may need to take an extra course beyond the major requirements to satisfy all the prerequisites for the capstone course. These projects usually combine hardware and software design with a multi-disciplinary team of engineers. It is rare for these projects to have a role for a biomolecular engineering student.

Some projects are funded by donations from industry, while others are funded by the students themselves. Student-generated projects generally require more fund-raising effort on the part of the students, as the industrially sponsored projects are usually proposed by the sponsor.