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Departments :: Biomolecular Engineering

Frequently Asked Questions

What is Bioinformatics?

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, DNA microarray chips, two-hybrid experiments, and tandem mass spectrometry.

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 training.

  • Tool Maintenance

    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 an excellent collection of pointers addressing the definition of Bioinformatics:

These articles describe some of our programs and areas of research:

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). 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 paradigm of engineering-preceding-science is actually quite common, but clashes with the popular meme that science precedes engineering.

What can I do with a Bioinformatics degree?

You can work at the interface between biochemistry, computer science, and mathematics, creating new solutions for high-throughput chemistry, designing analysis systems for drug design, and many other things. Our graduates in bioinformatics have not had any difficulty finding jobs. Our Ph.D. students have been sought for faculty positions. Take a look at our grad alumni page to see who has finished.

Are there any jobs?

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. We do have a list of the alumni of our grad program, with partial records of where they ended up.

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).

Who else offers a bioinformatics degree?

Several universities now offer bioinformatics degrees. Two good lists are at:

What degrees does UCSC offer?

We offer undergraduate and graduate degrees in bioinformatics:

What is the difference between the Bioinformatics degree and the PBSE Bioinformatics and Computational Biology track?

The PBSE track and the PhD in bioinformatics are almost identical, both in requirements and in admissions standards. Students take the same courses and have access to the same lab groups either way. The PBSE program was created because the grad admissions process at UCSC only allows students to apply to one program—the PBSE program provides a single-application admission to MCD biology, biochemistry, microbiology, and bioinformatics. If you are not sure whether you want to do one of those wet-lab fields or bioinformatics, the PBSE program allows greater flexibility.

Why do bioinformatics courses have a BME code, and what is the BME doing behind the cyberslug?

The bioinformatics programs are run by a department, Biomolecular Engineering, created Winter 2004 that houses two overlapping groups of researchers: bioinformatics and biomolecular engineering. BME is also the department that administers the multi-department undergraduate major in Bioengineering. The graduate program is now called Biomolecular Engineering and Bioinformatics, reflecting the twin focuses of the department and the synergy between the closely related fields.

How do I apply?

Graduate application is now done entirely through the web, at the UCSC Graduate Application Web Site. Undergraduates should check the Admissions Office web page. Graduate applicants should read the Graduate Admissions Page of the Jack Baskin School of Engineering.

When's the next application deadline?

Graduate students, check the UCSC Graduate Application Web Site. We usually have deadlines in mid-December for fall admissions, and we don't look at applications for admissions at other times. Undergraduates (freshman or transer), check the Admissions Office web page.

Should I send e-mail to the faculty whose labs I want to join?

Probably not. We don't admit students directly to labs, but have the first-year Ph.D. students do three lab rotations to increase their breadth of learning, to spark collaborations between labs, and to help students choose which lab to join. Sending your resumé to a faculty member gets you no favorable treatment, and sending it to all of them just irritates them (and may lower your chances of admission).

If you have a real research interest in one of the labs, and have some questions about a particular paper from the group that you have read, or some new ata you want to share, then please do send e-mail. We love talking with collaborators and potential collaborators. We like explaining our work to interested audiences. But we get a lot of e-mail, so we hate getting spammed by people who are just sending out e-mails at random to everyone in bioinformatics.

Do I need to take a Subject GRE exam?

We do not require a Subject GRE, since there is none that covers the wide range of material that we want our incoming students to know. We do require the general GRE exam, and (for foreign students from non-English-speaking countries) the TOEFL exam. If you have taken a Subject GRE exam in a relevant field, please do include that information, as the better picture of you we have, the better admissions decisions we can make.

Is my TOEFL score good enough?

Our program requires 570 on the paper-based test, 230 on the computer-based test, or 89 on the internet-based test for admission of foreign students (except those whose native language is English)—these are bare minimum scores, and foreign students we have admitted have generally had much higher scores.

Are my GRE scores good enough?

We don't have a hard cutoff for what GRE scores are required - good recommendation letters from people who have supervised previous research are always more important. All we can report is the average GRE scores for those who enrolled (Fall 2004 through Fall 2009): Verbal 624, Math 747, Analytic 4.37. Note that these averages include both MS and PhD students, with the PhD student usually being above these averages. To the extent that we care about GRE scores, all three are important, as students are more likely to fail from difficulty in writing a thesis than from difficulty in doing the computational parts of the research.

How much financial support do grad students get?

We generally provide full support for Ph.D. students and no support for M.S. students. The admissions offers usually come with information only about the first year, because we have to put the money on the table for those offers, and aren't allowed to gamble on getting grant renewals or other funding sources. In practice, every Ph.D. student has been supported for at least 5 years, though some have had to work as teaching assistants some quarters, when research grants ran out. Our M.S. students frequently get teaching assistantships also, usually from the large freshman courses of other departments (biology, math, computer science, statistics, etc), but we offer no promises to M.S. students.

We strongly encourage all grad students to apply for outside fellowships and grants, as the number of students we can teach is mainly limited the number we can afford to support.

What are my chances of admission?

The department has essentially no input into freshman admissions. The Admissions Office realizes that most undergrads end up changing their minds at least once about their majors, and so does not pay too much attention to what incoming freshmen say they want to do.

The department does have considerable say for transfer students. We expect students to have completed at least 6 core courses (2 calculus, 2 programming, 2 chemistry) with a GPA of 3.0. The more science, programming, and math students take before transfering, the better. Finishing the IGETC transfer curriculum is not a good idea, as it is better to leave some general education courses to leaven the otherwise heavy load of technical courses.

We really can't estimate graduate chances of admissions, as the strength of our applicant pool varies from year to year, as does the number of students we can afford to support. Here are a few approximate statistics:

Year foreign accepted US accepted (MS, no support) US accepted (PhD) US accepted (MS+PhD)
Fall 2012 9% 47%  50% 49% 
Fall 2013 8% 88% 38% 46% 
Fall 2014 14% 62% 36%  42%
Fall 2015 3% 36% 29% 30% 
Fall 2016 9% 30%  66%  52%

The reason for accepting so few foreign students has nothing to do with quality, just money. Some of our funding sources are limited to US citizens or permanent residents, and foreign students on visas always cost far more in tuition. When we face the choice of admitting one foreign student or 1.5 domestic students, the foreign student has to look at least 1.5x as good.

Note: we often admit students who apply to the Ph.D. program to the M.S. program (without funding). Some M.S. students later transfer to the Ph.D. program (with funding).

What is your relation to the UCSC Extension program in Bioinformatics?

The certificate program at the UCSC Extension in Silicon Valley is not the equivalent of either the undergraduate or graduate programs at UCSC and is not taught by UCSC faculty. It does help train people in industry in the field of bioinformatics, and it has served as an introduction to the field for students who later came to UCSC for the graduate program.

We also get a few people who live in the area who want to sign up for one or two of our grad courses through the Concurrent Enrollment program of the UCSC Extension. This is a program that allows students to register for one or two regular UCSC courses without being enrolled as a student. This is an excellent way for a re-entry student to test the waters, to see whether the graduate program is a good fit for them. It also provides the faculty with a lot of information about the student, which can be help make us make a good decision at admissions. We've had some excellent students join the program through this mechanism.

Can I get an internship?

Sorry, we do not offer internships.

What quarters are courses offered?

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 http://www.soe.ucsc.edu/courses/schedule/bme

The Courses menu in the left navigation panel of the SoE website gives access to the other department's annual schedule. Unfortunately, our colleagues in Physical and Biological Sciences are not so obliging, so finding out when biology and chemistry classes will be offered can be a challenge. The catalog http://reg.ucsc.edu/catalog/ provides some useful information about when courses are normally offered, but schedules can change each year.

What programming languages do you use?

We use Perl, C++, and C for most of our programming, though there are some programs in Java, Fortran, Python, TCL, and other programming languages. We are switching from Perl to Python for new students in our core bioinformatics course. Many of our computer experiments and pipelines are set up using gnu Make.

Does UCSC have a mailing list for bioinformatics announcements? A Facebook page?

We have several mailing lists for different purposes:

  • compbio
    Used for announcements of research seminars, updates on research progress, research opportunities, social events, and general-interest bioinformatics topics at UCSC.

  • 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, when they have a new genome released.

  • undergrad
    For weekly newsletter to undergraduates. To subscribe, contact advising@soe.ucsc.edu.

  • binf-ugrads
    For bioinformatics undergraduates (majors, minors, and premajors). Only bioinformatics faculty and advising staff can send to this mailing list. To subscribe, you must either officially declare the major or minor or talk with the School of Engineering advising office about your intent to declare and ask to be added to the mailing list.

  • binfgrads
    For official communications to Bioinformatics grad students. To subscribe, get accepted into the bioinformatics grad program.

  • Facebook
    There is now a Facebook page, which is used mainly by graduate students for purely social events.

As a grad student does the MCD bio seminar count as a way to meet the seminar requirement?

Definitely. Taking the MCD Bio seminar for a quarter, or the Chemistry seminar, or the Microbiology and Enviornmental Toxicology seminar is encouraged. Since we do not routinely have faculty attending all these seminars, and don't have access to attendance information, we would like some evidence that you actually attended the seminars. One good way to do that is to write a paragraph about each seminar each week, and turn them in to the grad director at the end of the quarter.

As a grad student, how many courses should I take?

Look at the load paragraph on the Graduate Requirements page, which explains typical grad student course loads.

As an M.S. student do I have to do a thesis?

Starting in Winter 2010, the M.S. capstone requirement has been reduced from a thesis to one-quarter research project with a written report. The easiest way to satisfy this requirement is to take a "lab rotation" (BME 296).

How long does the written report for the capstone of an M.S. student need to be?

Teachers always hate the question "how long should the paper be?", because the question rarely has a good answer. We want clear writing that covers the subject, and the length of that varies enormously with the subject.

There is no specific length or style requirement for the capstone paper. It should be thorough enough to cover everything done in the
lab rotation, and clear enough that it could be read by someone outside the lab group. Generally, it will be longer than journal article (more background, more discussion of things that didn't work out), but shorter than a thesis (less background, less total research).

Quarter-long projects that students have done in the past have generally taken 10-20 pages to write up. Students shouldn't be writing it all at the last minute, but should write a draft (incomplete though it has to be) halfway through the quarter. By that point they've generally got the background, probem statement, and some of the methods, but no results. Detailed feedback on this draft makes a huge difference in the quality of the final capstone report, and can provide the "needs to be more detailed" or "cut out the padding" feedback that helps determine the final length.

Note: all lab rotations should have a written report of this nature, just as all lab rotations have a final oral presentation. Part of the point of the lab rotations is helping students learn how to do research, which includes learning how to present it in writing and orally.

How do I sign up for lab rotations?

Ph.D. students have to do 3 lab rotations, and full-time students are expected to do these Fall, Winter, and Spring of their first year. M.S. students are expected to do 1 lab rotation in their two years, but those considering switiching to the Ph.D. program do 3 lab rotations. We're still working out a system for assigning Fall rotations, but for Winter and Spring we have a simple system. Near the end of Fall and Winter quarters, the students needing lab rotations are asked to submit a ranked list of labs they would like to rotate in. The grad committee then attempts to assign students to labs meeting as many of the first-choice requests as possible without overloading any lab. Students who do not get their first choices in winter have higher priority in the spring. Once assignments have been made, student can register for BME 296, using the section code for the faculty adviser of the lab they are rotating in.

As a Ph.D. student can I get an M.S. along the way? Do I have to?

Ph.D. students who are admitted to candidacy have automatically fulfilled the requirements of the M.S. degree, and we expect students to routinely file to get the M.S. at the same time that apply for admission to candidacy. There is no obligation to do so, but there is no reason not to.

What exam(s) do I need to take before advancing to PhD candidacy?

There are two exams in the catalog requirements: an oral qualifying exam at the beginning of the third year (usually Fall quarter) and the advancement exam by the end of the third year.

The oral qualifying exam consists of writing a 5-page research proposal (on a subject different from the anticipated PhD thesis), then answering questions presented orally by a faculty committee. The oral exam is not public (just the commitee and the student are present). For the oral exam, there will be a deadline for turning in your short proposal to the grad committee, who will put together a committee and schedule the oral exam. The committee can grill you on anything you have studied, but are likely to concentrate on core material or material specifically relevant to the proposal.

The advancement exam is a public presentation of a thesis proposal, explained in the answer to the next question.

On 30 Oct 2009, the faculty voted to waive the oral qualifying exam for any student who sucessfully advances to candidacy by the end of their second year. That is, students who have advanced by 1 Sept 2010 will not have to take the oral exam in Fall 2010.

How can I get a fellowship?

Getting a fellowship requires applying for one. We don't have many under our control (a tiny pot of money we use to fund students in their first year, allocated when we admit the students). For the most part, getting fellowships requires filling out application forms and writing essays, much like applying to colleges. We do provide some support. For example, there is a homework assignment in BME 205 requiring students to find a fellowship they are eligible for and write the application essays, and students get detailed feedback on their essays. We also have started a collection of successful fellowship applications by students in /projects/compbio/papers/fellowship-applications/ (not available on the web, for privacy reasons).

What do I need to do for a thesis proposal?

In order to advance to candidacy, Ph.D. students need to finish all their course work and present a thesis proposal, both in writing and in a public oral presentation. Almost all faculty and grad students come to the advancement talks—they are major events. We expect students to advance to candidacy at the end of their second year of grad school.

Examples of previous thesis proposals can be found in /projects/compbio/papers/thesis-proposals/ (not available on the web, as some of the proposed theses have not been completed yet). Many of these examples are longer than they should be, as the students were advancing far too late. We would have more examples if more students put theirs in the directory. Encourage your fellow students to share!

The point of a thesis proposal is to show that you have a clear plan for your thesis, that both you and your committee agree on what it will take to declare the thesis done, and that you are prepared to undertake the research you propose.

A thesis proposal should consist of a few simple things:

  • A clear statement of the research question being addressed. This is not just a general statement of the field the research will be in, but a particular hypothesis (or set of hypotheses) that will be investigated. It should also explain to people outside the field why the question is interesting.
  • A survey of what related work has previously been published. This section should be pretty thorough—it should be usable as a chapter of the final thesis (with some updates for subsequently published papers).
  • Prior work by the student. This is the part that is usually too long. Your advancement should come as soon as you have a clear idea what your thesis could be about—not when you are almost finished. Still, there is usually some initial research or data collection that lead to the ideas of your thesis, and this section is where you report it. The main point of preliminary data is to establish that you are capable of doing the intended research—not that you are almost done!
  • Plans for completing the thesis. You should have a clear set of goals with expected dates of completion for each part. If there is high-risk computational or wet-lab experimentation, you should have explicit backup plans for what you will do if experiments fail. Usually, a big chunk of the time spent by the thesis committee is negotiation with the student and the adviser about how much needs to be completed in order to have a complete thesis (sometimes the student is far too ambitious and outlines a 20-year project, more often the student is vague about when they'll stop—a thesis should not be an open-ended project, but have a clear stopping point, even if the underlying research is more open-ended).

There is no fixed length for a thesis proposal—they can vary from 20 to 100 pages, with the better ones usually 20 to 30 pages. Clarity and originality of thought, thoroughness of literature search, and specific measurable milestones are what we are looking for in a proposal.

The writing in the thesis proposal should be of journal quality. Be sure that your advisor has read through the entire proposal and approved it for distribution to other committee members to avoid duplication of work. Allow 4 weeks between the distribution to the committee and the presentation. Having another graduate student read through the proposal as well can be helpful to both of you, and similarly for preparing your proposal talk.

For preparing the the proposal, I recomend using LaTeX with the document class ucthesis, using the version in /projects/compbio/papers/tex/ucthesis-ucsc/ucthesis.cls , so that sectons and chapters of the proposal can be easily recycled in the final thesis.

Who needs to be on my advancement committee? my thesis committee?

The composition of the advancement committee is a bit tricky. You need 4 members:

  • your thesis adviser.
  • the chair of your advancement committee, who must be tenured and not your adviser.
  • an outside member, a tenured faculty committee member who is not in your department.
  • one other faculty member.

See the forms on the Graduate division web site for details. Note that it is possible to have a non-faculty Ph.D.level researcher as one of your committee members, but this requires more paperwork, generally including getting a CV from the person.

Your thesis committee is somewhat less constrained than the advancement committee, but it has been standard practice in the department to request that the advancement committee serve as the thesis committee. If you plan to have a different thesis committee, discuss this with your adviser, the advancement committee, the grad director, and the grad advising staff before your advancement exam.

How is the Advancement to Candidacy (ATC) exam structured?

The Advancement to Candidacy Exam in BME is primarily an evalution of the student's thesis proposal. The format of the exam is fairly simple:

  1. One month before the exam, the student distributes the written thesis proposal to the committee. Some faculty prefer paper copies, some prefer electronic copies—the student should check with the individual faculty members. Drafts of the proposal should already have been read and approved for distribution to the committee by the student's adviser—it is embarrassing for everyone if the adviser tells the committee that they are not willing to supervise the proposed work.
  2. The student presents their thesis proposal publicly in a one-hour oral presentation. It is the tradition of the department that all grad students and faculty who are in town and not scheduled with conflicting classes attend the advancement talks.
  3. After the public presentation, the committee grills the student in private, usually in the same room as the public presentation. This may cover material in the written proposal, the oral presentation, background material that the student should know, research plans, contingency plans, or any other material that the committee needs to know in order to determine whether the student passes.
  4. The committee deliberates in private without the student present. At this time the committee decides whether the student passes, passes contingent on making some corrections to the proposal, or fails. If the student passes, the committee signs the appropriate paperwork. In any case, the chair of the committee takes notes, in order to prepare the formal report on the exam, which is a 1- to 2-paragraph summary of the strengths and weaknesses shown. The formal report is filed with the School of Engineering grad advising staff.
  5. The student is called back in and the results presented to them. Any contingencies on passing are clearly spelled out (and generally provided by e-mail within a day).

How is the Advancement to Candidacy (ATC) exam judged?

The faculty on the advancement committee have to weigh several considerations:

  • Does the student have enough background knowledge and skill to do the proposed research? For the most part, the BME department relies on the required courses to provide adequate breadth, so the ATC exam concentrates on the knowledge needed for the specific research, but this often entails more breadth than most students realize, so students should be ready for questions on anything that they have (or should have) learned. A student who has completed the required courses, but still does not have sufficient knowledge may be required to take more courses.
  • If the proposed research were completed, would it be sufficient for a PhD thesis? A PhD thesis must make some original contribution to science or engineering. It is not enough to do a better implementation of an existing idea (though that is sufficient for an MS thesis). Sometimes students propose work that is just routine lab work or programming, with no indication of the novelty of the ideas. The thesis proposal should start with a clear statement of the new ideas that are being developed.
  • Can the research be completed in a reasonable time frame with available resources? Some students pick projects that would be really exciting if possible, but which can't realistically be done. These students usually get contingent passes or fails, and need to rework their research plans to be more reasonable. Here the committee is the student's friend, protecting them from themselves.
  • Is the research plan clearly stated, with clear indication of where the PhD thesis ends and post-doc work begins? A lot of students come to the exam with open-ended research plans that could take a lifetime to complete. This is useless for planning a PhD. Here the committee is the student's friend, protecting them from advisers who always want one more experiment. Having a clear statement about where the thesis research ends is important, and one of the main goals of a successful ATC exam is for the student, the adviser, and the rest of the committee to have agreed on the exact scope of the thesis.
  • Are there contingency plans in case experiments fail? Since PhD research is expected to be cutting-edge, and since the ATC exam is supposed to occur early in the research, there is a high probability that some of the proposed research will not have the expected results. Both wet-lab and computational experiments can fail. Students should have prepared some contingency plans for other approaches to the problem should experiments not work out or data that is expected from collaborators not be available. It is extremely common for students to be required to rework their research plans to include some discussion of alternatives should the rosy best-case plans they initially laid out not be realized. It is better for students to do this planning before giving the proposal to the committee.
  • Is the thesis proposal written well enough to give the committee confidence that the student can write a Ph.D. thesis, given the same level of assistance that they had for the proposal? Note that of the 4 C's of tech writing (clarity, correctness, conciseness, and completeness), Ph.D. theses put the most emphasis on correctness and completeness.
  • Is it clear what the candidate's contributions are, clearly separated from the research group's or adviser's contributions? The purpose of a Ph.D. thesis is to establish that the individual is capable of significant research contributions—thus it is essential that the proposal make it clear what the student has done and will do. A thesis or thesis proposal is no place for the generic "we" or passive voice. Whenever "we" is used, the names of the contributors should be given, and "I" should be used to emphasize the unique contributions of the candidate.