Gas station without pumps

2014 October 2

On senior theses

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Today is the first day of classes for us, but I’ve already been busy advising both new and returning students. Last week I sent out an e-mail message to the bioengineering and bioinformatics undergrads explaining the senior capstone options. I’ll probably have to send out a similar message each fall, so I thought I would save it here, where I can find it again.  It also might be useful for students and faculty elsewhere, as a lot of the advice is generic for any student starting a research project, though some is specific to our program and even to this year.
A lot of bioengineering seniors are starting senior theses now, a few bioinformatics seniors are, and most juniors will be spending a fair amount of time this year looking for a lab or a senior project, so I thought I’d address a few of the common concerns.  (I’m copying the BME faculty on this message, so they can see what advice I’m giving students.)

Bioengineering, bioinformatics, MCD bio, and other departments all have different expectations or requirements for their capstone projects (which can include senior theses).  I can’t talk for any programs except bioinformatics and bioengineering.


The bioinformatics capstone is generally satisfied by the project-based grad courses that are required, but some students (20%?) also do a one-quarter or more research or development project as a senior thesis.  These theses, since they are for short projects and not an essential part of the capstone are generally fairly informal, and only 20–40 pages long.  Students planning to go on to grad school are often well advised to do research projects, and the senior thesis is one mechanism for doing that.

Because bioinformatics theses are informal and not very common, most of this message will be about bioengineering theses.  Bioinformatics students may want to look through this message for ideas about how to join labs and find projects to do, but the main audience is bioengineering students.

Bioengineering senior theses are longer and more formal than the bioinformatics ones.  The research projects consist of at least 3 quarters of BME 195 plus BME 123T in Winter quarter (so 17 units, rather than 5 units for a bioinformatics thesis).  Partly this is because wet-lab work is much slower than computer work—turnaround time for an experiment may be days or weeks, rather than minutes or hours.

thesis or group project?

Bioengineering students have the option of doing a group project for a capstone (BME 123A/B) or a senior thesis.  Those planning to go on to grad school should probably choose the thesis option, as it is better preparation for grad school.  Those planning to go into industry may be better off with the group project, though a senior thesis can also be good preparation for industry work.

If you have an idea for something you want to design and build, and can interest other students in working with you, forming a team project may be the best way to go, as faculty generally are more interested in getting help with their many research projects than with close supervision of a student-initiated project.  The BME 123AB and CMPE/EE 129ABC courses are a good umbrella for student-initiated group projects.
finding a lab and a project
No one is going to hand you an assignment and say “do this as a senior thesis!”—you have to find the project yourself.  But we don’t expect novice researchers to come up with great ideas alone (some students do come up with great ideas, of course), and so there is help in finding projects.  Generally students find projects by working with grad students, postdocs, faculty, and other researchers in a lab, and chipping off part of a bigger project that the lab is working on.  It is possible to come up with your own original project and convince a faculty member to supervise it, but that is more commonly done as group projects than individual theses, because most interesting projects are simply too big for one person to do in one year.

For the usual method to work, you need to be in a lab before you start your senior thesis.  Generally, that means finding a lab and working in it your junior year.  Bioengineering students work in labs all over campus—almost any department in the School of Engineering or the Physical and Biological Sciences could have a bioengineering project (and there are some in Social Sciences as well).

So first you need to find out what research on campus is happening and what interests you—that should start freshman year. One good way to find out what is happening in research is to attend research seminars—every department has one, generally weekly.  These are free public seminars, which you can attend without being a member of the department, signing up for a class, or anything else formal. Many of them are also listed as courses on the class schedule, so that rooms can be assigned and grad students can get credit for regular attendance (you can sign up too, if that will help you attend regularly, but make sure that you do attend regularly if you sign up—failing a no-work class for failure to show up sends a really strong message to faculty and future employers).  I particularly recommend BME 280B, the BME department seminar,  in fall quarter, since it is dedicated to showing new grad students the range of research projects available for their rotations. (Other quarters usually have different themes and other departments have different ways of organizing their seminar schedules.)

Don’t limit yourself to BME, though, as the department is too small to have enough undergrad lab positions for all the bioengineering students—bioengineering students have also worked with faculty from MCD bio, Microbiology and Environmental Toxicology, Electrical Engineering, Computer Engineering, and probably several other departments.  Some students have even taken summer research positions elsewhere and expanded those projects into year-long senior theses.

Once you have identified some research teams that look like they would be fun to join, do some homework: read the papers coming out of the group, look at their posters on the walls, talk to students who work in the lab. Once you have a fair idea what questions they are addressing and what techniques they are applying, send email to the head of the lab (often referred to as the “PI”, which is jargon for “Principal Investigator” on grant applications).  Don’t ask immediately for a senior thesis, but introduce yourself and ask if you can sit in on lab group meetings.

You may need to check out several labs simultaneously your junior year, which can take a fair amount of time in a year when you have a fairly heavy course load.

After you have been attending for a while, you might see a project that no one in the lab has time to do (there are always more ideas than time to follow up on them in a good research group).  If the lab group still seems interesting after several meetings, arrange a meeting with the PI to try to outline a possible project for you to work on.  Generally this will be a fairly small project that could grow into a senior thesis, as the PI will not want to commit the resources for a full-year project until you have proven that you are competent and reliable.

switching from finding a lab to senior thesis

Once you have  project identified and a faculty member willing to sponsor the project, you need to write up a 1–2-page proposal outlining the project and submit it to the undergrad director (that’s me).  I have not yet denied any senior thesis proposal, but the exercise of getting down in writing what you plan to do is a very important one, particularly for communicating with your PI about the scope of the project, so I’m not going to treat these as unimportant paperwork.

If the PI has not previously supervised a bioengineering senior thesis, I want to talk with them (at least by e-mail) so that they have a clear understanding of our expectations for a senior thesis (which may be quite different from the expectations in their own department—note the huge difference between a bioinformatics and a bioengineering senior thesis, even within the BME department).

The proposal should be submitted the quarter before the 3 quarters of BME 195, which generally means in the spring or summer for projects that run FWS.

We are planning to create a 2-unit “pre-capstone” course this spring to aid students in putting together group projects and senior thesis proposals.  The course is optional, but is likely to be very useful in crystallizing somewhat vague ideas into productive capstone projects and forming working groups.
what is a bioengineering senior thesis?

A bioengineering senior thesis is modeled after a PhD thesis.  It is obviously smaller (a one-year project, not a 3–7-year project), and a senior thesis does not have to be “novel work” in the sense that a PhD thesis does.  You can do an implementation of someone else’s idea for a senior thesis, but there should be substantial engineering or scientific thought on your part—you should not be merely “hands in the lab”.

A bioengineering thesis can be either a scientific one or an engineering one.  The details of what you do in the lab are similar—the difference is mainly in the goal.  A scientific thesis tries to answer a question about the real world: “what does this protein do? what is the evolutionary history of this virus?”, while an engineering thesis has a design goal “how can I move DNA slowly through a nanopore in 3M KCl? How can a get a halophilic microorganism to produce substantial quantities of butanol?”  You may end up using the same lab techniques for either sort of thesis, and you can often spin the same project as either a science or an engineering project (a lot of “science” is really engineering new lab methods, and a lot of “engineering” requires discovering new science).

Since the bioengineering major is an engineering major, I try to help students view their projects as engineering projects, especially when they are working with a PI who sees them as science projects, but there is no requirement that a bioengineering thesis must be one or the other—either is acceptable.
format of a thesis

You must write up what you do in the format of a thesis: start with a brief statement of the design goal or research question, give a detailed background on what other people have done in the past and why the problem you are tackling is important, then give a detailed description of all the design or experiments you do, including the ones that fail (and how you debugged the failures).    You do need to distinguish clearly what you do from what other people on the project do—a thesis should be written with “I” not “we” (which is different from multi-author journal papers), because the purpose of a thesis is to establish your individual research abilities.  Avoid using passive voice for the same reason—we want to know what you did, not just what was done.  When you use passive voice in a thesis, you are denying that you did it, but failing to tell us who did.

You should be writing a draft of your thesis every quarter of BME 195 and submitting it to the PI for feedback on both the content and the writing.  The first quarter should result in a draft that has a clear statement of the research question or engineering design goals, a thorough literature survey explaining what other people have done and why the question or goal you are tackling is interesting and important, and a research or development plan for how you will answer the question or achieve the design goals.  Each subsequent quarter will result in editing and rewriting big chunks of the thesis, and replacing the research plan with the research results.

The audience for your thesis is not your PI, nor even other members of your lab team.  It is other bioengineering students who might want to join the team—so you can assume that your audience has a basic knowledge of biology and engineering, but not of the specifics of your lab team’s approach.  You need to define jargon the first time you use it, and you need to give a brief intro to any techniques that you use that aren’t covered in the required courses for bioengineering students.

A thesis is not a lab notebook or a lab protocol handbook (though you may wish to give detailed protocols in an appendix to the thesis).  We are interested in the engineering thought, not how many microliters of this or that you mixed for how long—unless your engineering is optimizing the protocol, in which case we need to know why you increased or decreased pH, temperature, salinity, or whatever else you were manipulating to do your optimization.

A thesis is not a journal article.  Journal articles are very limited in space, so are carefully trimmed and edited to remove any dead ends or interesting side trips that don’t appear to contribute to the final result. A thesis should include discussion of the entire project, including the side trips and dead ends.  We want to see how you solved problems, not just the final solution, which is all the journal article usually has room for.

In BME 123T winter quarter (generally in the middle of the thesis research), we will go through several drafts of your thesis, with detailed feedback on the writing (and somewhat less on the content than the PIs are expected to give).  You should be starting Winter quarter with a complete first draft (some parts will still be plans rather than results, of course), and coming out of BME 123T with an almost complete final draft, so the spring quarter can be dedicated to finishing the research, with only a few new results to be written up.

presentation requirements

The new curriculum requires a senior portfolio containing at least two projects, one of which is your capstone project.  (The other project is generally a small one from one of your required courses.)  The portfolio also requires PDFs of three different presentation modes: a final paper, slides for an oral presentation, and a poster.  You need to make sure that you have examples of all three formats for your senior portfolio—if you are missing one at the beginning of your senior year, find a way to create it during the year.

Everyone should be producing a poster for their capstone for the undergraduate symposium in the spring (though posters produced for other venues can be included in the senior portfolio instead).  The senior thesis requires a final paper and the group projects generally require an oral presentation.  BME123T is expected to concentrate mainly on the written report format, but if students need poster or oral presentation opportunities, the course can be used for those as well.

The BME department has agreed to pay for undergrad posters printed at BELS for senior projects or for conferences for bioengineering and bioinformatics students, but NOT RUSH FEES.  If you miss the deadlines for normal charges, then the rush fees come out of your pocket (unless you can sweet-talk your PI into covering them).

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