This page has be edited from a similar one that applied to the now-discontinued Bioengineering major. Those students finishing up the Bioengineering major will still find useful information here.
(Last Update: 2021 November 12 14:06 PST )
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—if you just want course work, you may be better off at a less research-focussed university. 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 like for students to remain in the lab long enough to be productive researchers, which generally means at least 2 years. A two-year timeline means that one of the first tasks for transfer students in biomolecular engineerin 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 some get involved much earlier.
Finding a lab doing interesting work requires some effort on your part, but we provide several tools to make this easier:
Seminars in other departments are also worth attending when there is a topic that looks interesting, as many BMEB majors end up doing research with faculty from other departments.
If you are interested in a lab, do not start by asking to join the lab as a researcher—that is a pretty big ask, and the PI is likely to say "no" if they don't already know you. Instead, ask questions about papers from the lab that you have read (showing that you are really 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 does not require much from the research group, yet fairly quickly results in the lab members and you knowing whether or not you would be a good fit for the lab. After you have been in the meetings for a few weeks, you can start volunteering to take on small tasks for the group and asking about research projects you can contribute to.
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 5 units, which require 15 hours of work a week for 10–11 weeks (150–165 hours total), while others are 2 units (6 hours a week, or 60–66 hours total).
All 5-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 2-unit independent study courses should have some form of end-of-quarter report for evaluation by the faculty member, but it may be much more informal than for 5-unit independent studies, at the discretion of the faculty member supervising the work—often one-on-one verbal reports from the student are acceptable for 2-unit independent studies.
Any reference to "faculty member" here includes not only Academic Senate faculty, but also lecturers and some senior research staff.
How students register for independent study courses (see https://undergrad.soe.ucsc.edu/current-students/independent-studies):
Starting Spring 2020, we are accepting email approval by faculty and undergraduate directors for independent-study forms.
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.
There are many different independent-study course numbers, with subtly different meanings. Each comes in two sizes: a 5-unit course, for which 15 hours a week of work is expected (150–165 hours total) and a 2-unit course, for which 6 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.
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.
Biomolecular Engineering students have four capstone options:
Students in the bioinformatics concentration must take the bioinformatics graduate courses as their capstone.
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 PhD programs in graduate school, as the senior thesis is deliberately structured like a miniature version of a PhD thesis, and so provides excellent training for grad 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.
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, a tiny explanation for why that 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 say who the faculty supervisor is, and that 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.
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:
Don't bury the lede! 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.
The research chapters should be logically organized with experimental methods, results, and discussion of the results placed close together, not widely separated. In most theses, results from one experiment drive the choice of which other experiments to do, and 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.)
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 slotted in from the final quarter of work (and any interpretation of those results).
Students doing a senior thesis are required to take BME 123T, a 5-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.
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 that 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.
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.
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.
Many CSE and ECE group capstone projects are suitable for bioengineering (BENG) 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.