Frequently Asked Questions: Biomolecular Engineering and Bioinformatics

What is Biomolecular Engineering?

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.


What is Bioinformatics?

Bioinformatics is the use of computers and statistics to make sense 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:

  • Tool Building: Creating new programs and methods for analyzing and organizing data. This is where our graduate program is focused.

  • Tool Using: 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.

  • Tool Maintenance: Setting up databases, translating biologists' questions into databases 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.

View a collection of information addressing the definition of Bioinformatics.

The Biomolecular Engineering faculty members are involved in extensive research across a number of of areas - view more information about ongoing research.

What degrees does UCSC offer?

The BME Department at UCSC offers several undergrad and graduate programs. The Ph.D. program is part of the Ph.D. Program in Biomedical Science and Engineering, as the Biomolecular Engineering and Bioinformatics track.


What is the difference between Bioinformatics and Computational Biology?

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). Read a good defense of this distinction by Russ Altman. You can do either style of bioinformatics at UCSC, but we feel 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 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.


How do I get involved in research?

We strongly encourage undergraduates to get involved in research. UCSC has an unusually large ratio of undergraduate students to graduate students for a research university, so we offer more opportunities for undergrad research than almost anywhere else;  it is up to students to find and pursue the opportunities. View independent study and Research Lab info for more information about finding and joining a research group.


How do I contact faculty?

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. 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.

Responses are typically 24 hours or more from receipt of the email.


Can I take courses P/NP (pass/no-pass)?

BMEBBS majors must take all major courses for a grade. Note: special exceptions were made by the faculty for Fall 2019, Winter 2020, and Spring 2020, allowing P/NP grades for those quarters only.


Do I have to take BME 21L?

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.


Do I have to follow the latest catalog?

View the official catalog for the BMEBBS degree. From this catalog page, you can view older catalogs and their requirements. Students have "catalog rights", which allow students 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 starting at UCSC; 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 you can also view graphical summaries, or "curriculum charts", including archives of older sets of requirements. If the curriculum chart and the corresponding catalog disagree, the catalog takes precedence (please notify advisors to the discrepancy).


What quarters are courses offered?

The Jack Baskin School of Engineering supplies a schedule of courses (grad and undergrad) offered each quarter for the current year.

Additional 2021-2022 Curriculum Charts:

You can also search for course availability for the current quarter, the next quarter, or past quarters.


I see that graduation requires an exit interview and a senior portfolio. How do I submit them?

A bioengineering B.S. portfolio is required for graduation. 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 in 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 program changes made over the past several years have been in response to these student comments, as the department continually strives to improve the program. 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.


What programming languages do you use?

We use Python, C++, and C for most of our programming, though there are some programs in Perl, R, Java, Fortran, and other programming languages.


Does UCSC have a mailing list for bioinformatics announcements?

We have several mailing lists for different purposes:

  • undergrad
    All majors and proposed majors 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 by making a request online.

  • 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.

  • genome-announce
    Infrequent postings by the genome browser staff, such as when they have a new genome released.
  • Facebook
    The Facebook page is used mainly by graduate students for purely social events.


What can I do with a BMEBBS degree?

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 M.S. 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 Ph.D. 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. Many graduates start their careers with their B.S., then, with some insight from work experience, enter grad school to specialize.


Are there any jobs?

The department doesn't track job openings, but we frequently get calls inquiring about faculty and grad student availability. View a number of job boards:


Can I get an internship?

We do not offer internships. You can inquire at the Career Center for resources or finding industry internships. 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.

The Federal government supports quite a bit of research experience for undergraduates — for example, through the NSF REU program and The Department of Energy's Workforce Development for Teachers and Scientists.


Where can I go to grad school?

Several universities now offer bioinformatics degrees; view a list from the International Society for Computational Biology.

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.