(Last Update: 2021 November 11 11:20 PST )
This web page is a frequently-asked-questions page for the Biomolecular Engineering and Bioinformatics Bachelor of Science (BMEBBS) program at UCSC. It is currently a rough draft, but should be completed some time during Fall 2021.
Biomolecular engineering is the design of biomolecules (DNA, RNA, proteins, … ), metabolic pathways, signaling pathways, cells, and the instrumentation for measuring them. It is the engineering side of sciences like biochemistry and molecular biology.
There are many different applications of biomolecular engineering, including monoclonal antibody therapy (for COVID, for example), immune checkpoint inhibitors, mRNA vaccines, growing birth control hormones at home, making vaccines heat stable, … . Instrumentation includes sequencing methods (like nanopores), sensing (like nanopipettes or electrical monitoring of cortical organoids), manipulation of cells (with nanopipettes and ion pumps), and remote-controlled microscopes and lab setups.
Bioinformatics is the use of computers and statistics to make sense out of the huge mounds of data that are accumulating from high-throughput biological and chemical experiments, such as sequencing of whole genomes or of expressed RNA, DNA microarray chips, two-hybrid experiments, and tandem mass spectrometry. Our expertise at UCSC concentrates heavily on sequence data—both short-read sequence data (say from Illumina sequencers) and long-read sequence data (especially nanopore data). There is a lot of cutting-edge work in genome assembly, alignment of genomes, and machine-learning applied to analyzing genomic and transcriptomic data.
There are three different approaches to bioinformatics:
Creating new programs and methods for analyzing and organizing data. This is where our graduate program is focused.
Using existing programs and data to answer biologically interesting questions. We believe that this type of bioinformatics does not need a separate degree, but should be part of every new biologist's or biomolecular engineer's training.
Setting up databases, translating biologists' questions into ones that programs can answer, keeping the tools working and the databases up to date. The undergraduate program prepares students for this role in industry, as well as for going into graduate school.
This page has a decent collection of pointers addressing the definition of Bioinformatics:
The research areas of the faculty in the department can be found on the department research page: https://engineering.ucsc.edu/departments/biomolecular-engineering/research.
The BME Department at UCSC offers several undergrad and graduate programs, listed at https://engineering.ucsc.edu/departments/biomolecular-engineering/degree-programs. The Ph.D. program is part of the Ph.D. Program in Biomedical Science and Engineering, as the Biomolecular Engineering and Bioinformatics track.
Our department considers bioinformatics and computational biology to be essentially synonymous, but some people make a distinction between two flavors of bioinformatics: tool and method development (bioinformatics) and applying existing tools to new biological questions (computational biology). There is a good defense of this distinction by Russ Altman. You can do either style of bioinformatics at UCSC, but we feel that the best work results from people who do both: developing new methods and applying them to new biological questions. One interesting thing about bioinformatics is that the fundamental work that opens up new fields is usually "engineering", while the application of the tools is "science". This engineering-preceding-science paradigm is actually quite common, but clashes with the popular meme that science precedes engineering.
We strongly encourage undergraduates to get involved in research, as research opportunities are the main value added by a University of California education over other, cheaper alternatives (such as California State University) UCSC has an unusually large ratio of undergraduate students to graduate students for a research university, so there are more opportunities for undergrad research than almost anywhere else, but it is up to students to take the initiative to find and pursue the opportunities. The independent-study page and BME 55 page provide more information about how to go about finding and joining a research group.
The faculty are listed at https://engineering.ucsc.edu/departments/biomolecular-engineering/faculty. That site provides office locations, phone numbers, and email addresses. Faculty generally have one or two open office hours a week, which are announced on their course syllabi, but can be a bit difficult to figure out if you are not in one of their courses (especially now that many faculty have Zoom office hours).
The best way to reach faculty for a quick question or to set up an appointment is to send them email. You should always use your @ucsc.edu email address when emailing faculty, as FERPA (a federal privacy law) prohibits us from talking about your student records except with you, and other email addresses could be anyone pretending to be you.
Use full, grammatical sentences in your emails to faculty, and start with the request you are making—faculty get a lot of email and don't want to wade through a lot of back story to try to figure out what you are asking of them. Be sure to include your full name (and what class and section you are in, if you are in one of their courses), as the @ucsc.edu email addresses don't always have your name associated with them.
Don't expect instant responses—the next business day (or 24 hours, whichever is longer) is considered a fast response to email.
The catalog says that BMEBBS majors must take all major courses for a grade, but special exceptions were made by the faculty for Fall 2019, Winter 2020, and Spring 2020, allowing P/NP grades for those quarters only.
Because we were unable to offer BME 21L in 2019–20 or 2020–21, we allowed students graduating from Spring 2020 to Summer 2021 to replace the BME 21L lab course with a different course. That exception is no longer available, and students in the biomolecular engineering concentration are expected to take the full BME 21L, 22L, 23L sequence—even if they have to take it out of order.
Students who have significant molecular biology lab experience elsewhere (from a job, working in a research lab, or coursework elsewhere) can petition to have that lab work replace BME 21L. Several community-college courses have already been articulated for incoming transfer students.
The official catalog for the BMEBBS degree is at https://catalog.ucsc.edu/Current/General-Catalog/Academic-Units/Baskin-School-of-Engineering/Biomolecular-Engineering/Biomolecular-Engineering-and-Bioinformatics-BS, but there is box at the top of that page that lets you see older catalogs and their requirements. Students have "catalog rights" (explained at https://catalog.ucsc.edu/Current/General-Catalog/Undergraduate-Information/Undergraduate-Academic-Program/Major-and-Minor-Requirements/Catalog-Rights), which allow them to choose to some extent which catalog they are following for each major, minor, or general-education requirement. Generally, students can use any catalog since they started at UCSC, but there are some exceptions for transfer students and for students that take a leave of absence. Although different catalogs can be used for each category (major, minor, gen-ed), a given major must follow a single catalog.
The catalog copy is the official word on the requirements, but can be a bit difficult to digest. Graphical summaries are available as "curriculum charts" at https://undergrad.soe.ucsc.edu/curriculum-charts, including archives of older sets of requirements. If the curriculum chart and the corresponding catalog disagree, the catalog takes precedence (but please point out the discrepancy to the advisers and undergrad directors, so that it can be fixed).
The Jack Baskin School of Engineering puts up a schedule of what courses (grad and undergrad) are offered each quarter for the current year. Those for our department are at https://courses.soe.ucsc.edu/courses/bme and the left-hand navigation panel gives access to the other departments' annual schedules.
MCD Biology's 2021–22 curriculum plan is at https://mcd.ucsc.edu/academics/courses/curriculum-plan-21-22.html, Chemistry's is at https://www.chemistry.ucsc.edu/academics/courses/curr_plan_21-22.html, and Microbiology and Environmental Toxicology's is at https://www.metx.ucsc.edu/academics/class-schedule.php?d=METX.
For looking at what is available for the current quarter, the next quarter (startling a little before registration opens), or past quarters, https://pisa.ucsc.edu/class_search is the most useful.
The portfolio is submitted on the web page https://engineering.ucsc.edu/departments/biomolecular-engineering/bioengineering-bs-portfolio. The portfolio has to include your capstone project and at least one other project. You also need to provide at least one PDF document for each of three formats: a written report, slides for an oral presentation, and a poster. You do not need to have all three formats for each project—it is enough to have one document of each format when all projects are combined. Normally, the capstone will have at least a written report. The portfolio is due at the end of exam week for the quarter in which you are graduating.
The senior-exit interview is a chance for students to provide feedback to the department about their experiences in the program. Many of the changes that have been made over the past several years have been in response to these student comments, as the department continually tries to make the program better. The interviews are held as group sessions and are scheduled by the undergraduate director. A few weeks before the end of each quarter, a Doodle poll (or equivalent) is sent to all the students who have declared their intention to graduate. Please apply to graduate by the first deadline, so that we know whom to poll. For summer graduation, interviews are held only after Session 2.
One, two, or more times are selected to try to cover everyone's availability, the times are announced, and students sign up for one of the interviews (generally through SignUpGenius or equivalent). The interview itself takes an hour or two.
We use Python, C++, and C for most of our programming, and the biomolecular engineering concentration mostly relies on Python, but there are some courses and research projects that use MATLAB, R, or Perl. Very occasionally, one might see FORTRAN, Java, or Javascript—mainly for research projects sponsored by other departments.
We have several mailing lists for different purposes:
undergrad
For weekly newsletter
to undergraduates from advising staff. All majors and proposed
majors in BSoE should get this newsletter automatically.
To subscribe, contact advising@soe.ucsc.edu.
bmeb-ugrads
For
undergraduates (majors, minors, and
proposed majors) in any of the BME Department's programs (BMEBBS,
BIOTBA, BMEB minor, and the discontinued BENGBS).
Only BME faculty and advising
staff can send to this mailing list, and almost all email comes
from the undergraduate director.
Those who officially propose or declare a major or minor are
automatically added to the mailing list (after a quarter or
two of delay), but any @ucsc.edu address can be added on request on
the web page.
compbio
Used
for announcements of research seminars, updates on
research progress, research opportunities, social
events, and general-interest bioinformatics topics at UCSC.
Any @ucsc.edu address can be added on request at the web page.
genecats
Used
by the genome-browser developers to share tips, describe
new features, discuss problems, and provide progress
reports. To subscribe, join the genome-browser research
and development group.
Facebook
There
is now a Facebook page, which is used mainly by graduate
students for purely social events.
You can work at the interface between biochemistry, computer science, and mathematics, creating new solutions for important 21st-century problems.
Our graduates in the bioinformatics concentration have not had any difficulty finding jobs, as our undergraduate training is the equivalent of an MS degree in bioinformatics at many institutions. They are generally able to join research groups (as a "captive" bioinformatician) or core bioinformatics groups at larger institutions. Those who want to do substantial new tool development usually continue on to get a PhD in bioinformatics.
The students in the biomolecular engineering concentration are competing with the much larger numbers of MCD Biology students for essentially the same jobs. We try to prepare BMEB students for the job market by emphasizing marketable skills: lab skills, bioinformatics, programming, and heavy-duty statistics. While the majority of the biomolecular engineering students take jobs soon after their B.S. degree, many continue on to get higher degrees. Quite a few do a few years of work with the B.S., then go to grad school once they have decided what they want to specialize in.
We have never tracked our B.S. graduates, but we were, for a while, keeping track of all our Ph.D. alumni. Take a look at our grad alumni page to see when they finished and pointers to many of their theses.
We don't keep track of jobs ourselves, but frequently get calls either trying to hire us or trying to hire away our grad students. There are some good web sites out there that you might want to check:
You can find even more sites by googling bioinformatics (jobs or career).
Sorry, we do not offer internships. You can ask at the Career Center for resources they have for finding internships in industry, but you will have to do a lot of the search yourself. There are many research opportunities in the labs of faculty on campus—both in the BME department and in other departments (MCD Biology, METX, EE Bio, … ), and some of these research opportunities include summer support. You can find more information about research opportunities at the undergrad research website: https://ugr.ue.ucsc.edu/.
One resource particularly worth looking at is the UCSC Genome Institute's Research Mentorship Internship program.
The Federal government supports quite a bit of research experience for undergraduates—for example, through the NSF REU program (https://www.nsf.gov/crssprgm/reu/) and The Department of Energy's Workforce Development for Teachers and Scientists (https://science.osti.gov/wdts/).
There are four choices of capstones for the biomolecular engineering concentration, and some of them require preparation as early as the second year of studies. More information can be found in a separate web page discussing independent study and capstones.
Several universities now offer bioinformatics degrees. Two good lists are at:
Students in the biomolecular engineering concentration end up in several different sorts of graduate programs: MCD biology, biomedical engineering, microbiology, and even medical schools (though students wanting to do medical, dental, or veterinary school will probably need to take a few extra courses—consult with the "Pre-Health" team at Career Services (https://careers.ucsc.edu/health/).