BINF 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:

• What is Bioinformatics?

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

• An overview of many of our research projeents 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:

• What is Bioinformatics?

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

cts.
• “Engineering school offers new major in bioinformatics”
• “Genome scientists muster computer software tools for handling the flood of raw data from the Human Genome Project and related efforts”
• “Bioinformatics experts gain ground in protein sequence analysis”
• “Take the protein challenge”

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:

• International Society for Computational Biology, Job Listings
• Biotech Find
• BioPlanet
• BioSpace Career Center Search for bioinformatics or computational
• JobSearchTech
• Color Base Pair
• Hire Bio
• Future Bio Jobs
• Bioinform
• Canadian Bioinformatics Jobs
• Bioinformatics Jobs in the Boston Area
• Georgia Tech "Career Outlook in Bioinformatics"
• Science Magazine's Listing of Bioinformatics Job Ads (mainly faculty positions)

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:

• http://ils.unc.edu/informatics_programs/doc/Bioinformatics.html
• http://www.iscb.org/iscb-degree-certificate-programs

What degrees does UCSC offer?

We offer undergraduate and graduate degrees in bioinformatics:

• A B.S. in Bioinformatics. Appropriate high school preparation includes mathematics, biology, and chemistry.
• A minor in Bioinformatics. This minor is suitable for biology and chemistry majors or for computer science and computer engineering majors.
• M.S. in Bioinformatics. Our master's students are generally accepted without financial support.
• Ph.D. in Bioinformatics. Our Ph.D. students usually receive full support.
• Our combined B.S. and graduate program in Bioinformatics allows our undergraduate majors to complete their graduate degrees in a somewhat condensed timeframe.
• The Ph.D. Program in Biomedical Science and Engineering has a Bioinformatics and Computational Biology track that is very similar to our Ph.D. program (essentially the same faculty and courses).  There are some very minor differences in admissions and requirements.  There are some cultural differences, as PBSE is dominated by MCD biologists, but the programs may merge in a few years.

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. Soon, the BME department will have another graduate in biomolecular engineering.  BME is also the department that administers the multi-department undergraduate major in Bioengineering.

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.

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.

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, ...), 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:

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 2 domestic students, the foreign student has to look twice as good.

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?

Some people send us requests for internship positions—sorry we don't have any, but US undergraduates are advised to check out the Summer Undergraduate Research Fellowship in Information Technology (SURF-IT) program.

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. See http://www.soe.ucsc.edu/mailman/listinfo/compbio for information about the compbio mailing list and to subscribe.

• 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. See http://www.soe.ucsc.edu/mailman/listinfo/genecats for information about the genecats mailing list.

• School of Engineering undergrad mailing list

  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. (See http://www.soe.ucsc.edu/advising/graduate/grademail.html for more information about graduate mailing lists.

• 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.

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 by the end of the second year and the advancement exam by the end of the third year.

The oral qualifying exam consists of writing a 10-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).

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 their 5th registered quarter.

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.

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.
• 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.
• 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.

The composition of the advancement committee is a bit tricky.  You need 4 members, including one outside your department.  The outside member should be tenured.  The "chair" of your advancement committee is not your adviser and must be tenured. See the forms on the Graduate division web site.

How do I get rid of those irritating "fly-out" menus?

The faculty were sufficiently irritated by the fly-out menus that the Web designers put in a secret mechanism to mollify them, while keeping the dysfunctional flyout style for everyone else.  In tiny grey-on-grey print in the footer of every web page on the Baskin School of Engineering, there are the words "Basic menus".  Clicking on these words gets rid of the fly-out menus.  Unfortunately, it is not sticky, so you'll have to keep doing it over and over.  Thus do web designers get their revenge on the web users of the world.