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2015 March 14

Not been blogging much

Those who have been following my blog for a while may have noticed that my blogging frequency has dropped quite a bit for the past few months.  I had planned to blog after every class meeting of the freshman design seminar, as I did last year, but I’ve simply been too busy. In addition to teach the freshman design seminar, I was also teaching the senior thesis writing course. Although both of these are 2-unit courses with small numbers of students (so the department gets essentially no additional resources as a result of my teaching them), they are both somewhat time-consuming, though the senior thesis writing much more so than the freshman design.

This weekend is the first weekend that I did not have a stack of thesis drafts to provide detailed feedback on (I’ve been averaging over 6 drafts a week to comment on all quarter).  In addition to the thesis drafts, I also arranged to have a 20-minute individual meeting weekly with each of the 19 seniors writing theses this year.  Because the meetings often ran over, I spent about 7 hours a week on those meetings.  I started each meeting with the student giving me a 2-minute elevator talk (after telling me what audience they were addressing the talk to and with what purpose). This served two purposes: to get the students to practice concise descriptions of their projects and to remind me which of the 19 projects we were talking about. (Several pairs of students were doing closely related projects in the same lab, so it was really easy for me to mix up the projects—and I have almost no memory for faces and names, so I needed the prompts!)

Next weekend I’ll pay for this weekend off—I’ll have all 19 theses to grade between Thursday night and Tuesday morning.  I won’t be doing as detailed feedback on this round—first, because there aren’t enough hours to do 2–3 hours a thesis; second, because I suspect that half the students won’t come by my office to pick up the graded theses (even those who still have a quarter to go before their theses are complete).

I hope to have the freshman design course all graded before the senior theses come in—they have their last lab on Monday and their design reports are due Tuesday.  The freshman reports are much shorter than the senior theses, so I can probably get them all graded on Wednesday.  If I get them done in a timely manner, I may take the time to try to do an end-of-quarter summary of the freshman design project course, which I think ran more smoothly this year, though not quite in the direction I had originally thought we would go.

This weekend, I’m getting back to work on my book, since I want to release a draft for the applied electronics course that starts in 2 weeks. I at least want the chapters and labs for the first two weeks to be finished, with no major overhauls planned for the remainder. I spent about 4 hours on the book today (after goofing around for a while with some phototransistor circuits that aren’t really relevant to the course—I’ll probably blog about that when I have more time, but it will take about 8 hours to do a good blog post on it, and I don’t have that much spare time this week). I hope to have the schedule for all the labs finished this weekend also—I made a good start on that in December, when I last had time to work on the book.

Next quarter will not give me much writing or blogging time—instead of the 12 contact hours (plus office hours and grading) that I had this quarter, I have 19 contact hours (3.5 hours of electronics lecture, 12 hours of electronics lab, 3.5 hours of banana slug genomics) plus grading 15 prelab assignments and 15 design reports a week for the electronics course. I’m hoping I can convince my co-instructor to do what grading we’ll need for the banana slug genomics, or that we won’t assign much that needs grading.

Also Spring quarter is when most students declare their majors, so I’ll probably have to increase my office hours from 2 hours a week to 3 or 4 to handle the advising load.  Two hours a week was just about right this quarter, especially since I allowed students to reserve a place in line by email.  I only had an empty office once or twice, and only ran an hour over once or twice.

On the administrative side, at least I’ve gotten the 20-page bioengineering self-study  and my 3-page contribution to the bioinformatics self-study done, so I won’t have too much to do on those next quarter.  The Curriculum Leave Plan is done for next year, and I hope it won’t need further modification. I’m reducing my teaching load next year to merely heavy (from insane this year), and some of the buyouts we had counted on for paying lecturers are not coming through, so the department has a structural deficit of about $30k, and only enough reserves to cover that for a couple of years (with no way to replenish the reserves).  I don’t know what we’re going to do long term, as we need to add more offerings of some of our more popular courses, at a cost of about $20k each.

2015 February 11

Still more senior thesis pet peeves

Filed under: Uncategorized — gasstationwithoutpumps @ 21:33
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I previously posted some Senior thesis pet peeves and More senior thesis pet peeves. Here is another list, triggered by a couple of groups of second drafts (in no particular order, though some are repeats of earlier ones—the students hadn’t gotten the message):

  • Passive voice is not to be used. When passive voice is used, the reader has a hard time figuring out who actually did anything. A thesis is written toestablish that someone is competent to do research and write about it. If the entire thesis is written in passive voice, with no first-person singular, the implication is that all the work was done by person or persons unknown.If you did the work, claim it! If you didn’t do the work, tell me who did!
  • “however”≠”but”: “However” is a sentence adjective, but it is not a conjunction. “However” is best used in the middle of a sentence—it can, however, be moved to the beginning, if necessary for readability. However, there is some danger when it is at the beginning of a sentence of merging the sentence with the previous one, and treating it like a conjunction. If you make that mistake, replace “however” and the following comma with “but”.
  • A number of students are using dangling modifiers: starting sentences with modifiers that would apply to the subject of the sentence, then changing their mind and putting a different subject in the main part of the sentence.  (I won’t embarrass students by quoting their work here—there are a number of examples at
  • Lists need to consist of parallel items.  The items need to be grammatically parallel as well as semantically parallel. If one is a noun phrase, then all need to be noun phrases.  If one is a verb clause, they all need to be verb clauses.  The semantic parallelism is a little subtler—don’t mix properties of an object with instructions for using the object, for example.  The bulleted lists of visual aids for talks are a particularly important place to apply the rules of parallelism.
  • I recommended that students start each chapter on a new page. Not only is this conventional book and thesis formatting, but starting each chapter on a new page makes it easier for the reader to distinguish between chapter breaks, section breaks, and subsection breaks.  Anything that makes it easier for a reader to stay oriented in a large document is useful. (I also recommended numbering sections and subsections with the chapter.section.subsection style used in most computer-science documents.
  • Figures and tables should be sequentially numbered, and the name of the figure is the word “Figure” followed by an unbreakable space, followed by the number. Because this is the name of the figure, it is capitalized like other proper nouns: Figure 1, Table 3, … . All figures should be referred to in the text, and the figures should appear near where the first reference to them is (unless there are a group of figures relegated to an appendix, with their existence mentioned in the main body, but not discussed there). If you need to insert a new figure, you need to renumber everything after that point—so make all your figure numbering be handled by automatic cross references by the program, as manual renumbering is highly error-prone. If you have a name like Figure 2b, it means a subfigure of Figure 2, not a figure you added late between the old Figures 2 and 3.  (Incidentally, I hate how WordPress throws away unbreakable spaces when converting back and forth between “Visual” and “Text” editing.  No matter how carefully I put them in, WordPress manages to mess them up and turn them back into ordinary spaces.)
  • “parse”≠”scan”: Every year I get a number of students who have picked up the word “parse” from a computer science class, and misunderstood it to be a synonym for “scan”. That’s not what it means. To parse something is to determine its structure—to break it into parts and analyze the relationship among the parts (generally in terms of some grammar). The verb “parse” is transitive—it takes an object, not a prepositional phrase, that holds the thing being analyzed.
  • Students are still having trouble with countable and uncountable nouns. For some students, this is understandable, as their native languages do not make the countable/uncountable distinction that English does.  I pointed students to the Oxford Student Dictionary of American English, edited by Hornby, which is now out of print, as being a dictionary that actually tells you whether a noun is countable or not.  The Oxford Advanced American Dictionary for learners of English is not as nicely formatted, but also has the [C] and [U] markings and is still in print.I used two examples of nouns that changed meaning depending on whether they were countable:  “grub” and “time”.  “Grub” is food, but “a grub” is the larval form of an insect, which may or may not be food. “Time”, when uncountable, is a duration, but “times”, when countable, are separate events.

    Even native speakers of English sometimes mess up the countable/uncountable distinction (though usually not with articles). The contexts where native speakers mess up are “amount of”/”number of”, “less”/”fewer”, and “much”/”many”—in all of which the first form should be used with uncountable nouns and the second with plural forms of countable nouns.

2015 January 26

More senior thesis pet peeves

Filed under: Uncategorized — gasstationwithoutpumps @ 22:17
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I previously posted some Senior thesis pet peeves. Here is another list, triggered by another group of first drafts (in no particular order):

  • An abstract is not an introduction. Technically, an abstract isn’t really a part of a document, but a separate piece of writing that summarizes everything important in the document. Usually the abstract is written last, after everything in the thesis has been written, so that the most important stuff can be determined. Most readers will never read anything of a document but the abstract.
  • Every paragraph (in technical writing) should start with a topic sentence, and the remaining sentences in the paragraph should support and expand that topic sentence. If you drift away from the topic, start a new paragraph! The lack of coherent paragraphs is probably the most common writing problem I see in senior theses.
  • I don’t mark every error I see in student writing. It is the student’s responsibility to learn to recognize problems that I point out and to hunt down other instances themselves. Students need to learn to do their own copy editing (or copy edit each other’s work)—I’m not interested in grading my own copy editing on subsequent drafts of the thesis.
  • Every draft of every document that is turned in for a class or to a boss should have a title, author, and date as part of the documents.  Including this meta-information should be a habitual action of every engineer and every engineering student—I shouldn’t be seeing last-minute hand-scrawled names and titles on senior thesis drafts.
  • Page numbers!  Every technical document over a page long should have page numbers. If you don’t know how to get automatic page numbers with your document processor, either stop using it or learn how!
  • Earlier this quarter I said that I did not care what reference and citation style you used, as long as it was one of the many standard ones. I’ve decided to change my mind on that—I do care somewhat what style you use for the reference list. Use a reference style that contains as much information as possible: full author names, full journal name, dates, locations of conferences, URLs, DOIs, … .  You may format it in any consistent manner, but provide all the information.
  • Use kernel density estimates instead of histograms when showing empirical probability distributions. My previous post explains the reasons.
  • Avoid using red-green distinctions in graphics. About 6% of the male population is red-green colorblind. There are color-blindness simulators on the web (such as that you can use to check whether your color images will work.  Modern gene-expression heat maps use red for overexpression, blue for underexpression, and fade to white in the middle.  This scheme has the advantage of having the strong signals in saturated colors and the weak ones in white or pastels, blending into the white background.
  • Comma usage continues to be a problem for many students. I discussed three common comma situations in English:
    • Comma splices. Two sentences cannot be stuck together with just a comma—one needs a conjunction to join them. If a conjunction is not desired, an em-dash can be used (as in the previous sentence). Sometimes a semicolon can be used, but never a bare comma.
    • Serial comma. There are two different conventions in English about the use of commas before the conjunction in a list of three or more items. In American English, the comma is always required, but in British English the comma is often omitted. I strongly favor the American convention (also known as the serial comma or the Oxford comma), and I will insist on it for the senior theses—even for those students raised in the British punctuation tradition.
    • When using “which” to introduce a relative clause, the clause should be non-restrictive. That is, omitting the clause beginning with “which” should not change the meaning of the noun phrase that is being modified by the relative clause. Non-restrictive relative clauses should be separated from the noun phrase they modify with a comma. If you have “which” without a comma starting a relative clause, then check to see whether you need a comma, or whether you need to change “which” to “that”, because the clause is really restrictive. Note: “which” is gradually taking over the role of “that” in spoken English, but this language change is still not accepted in formal writing, which is more conservative than speech.
  • The noun “however” is a sentence adjective, but it is not a conjunction. You can’t join two sentences with “however”. You can, however, use it to modify a separate sentence that contrasts with the previous one.
  • Colons are not list-introducers. Colons are used to separate a noun phrase from its restatement, and the restatement is often a list. The mistaken notion that colons are list-introducers comes from the following construction: the use of “the following” before a list. The colon is there because the list is a restatement of “the following”, not because it is a list. Note that two sentence back, I used a colon where the restatement was not a list. Similarly, I don’t use a colon when the list is
    • the object of a verb,
    • the object of a prepositional phrase,
    • or any other grammatical construct that is not a restatement or amplification of what came before the colon.
  • Most students in the class use “i.e.” and “e.g.” without knowing the Latin phrases that they are abbreviations for. I suggested that they not use the abbreviations if they wouldn’t use the Latin, but use the plain English phrases that they would normally use: “that is” and “for example”. If they must use the Latin abbreviations, they should at least punctuate them correctly—commas are needed to separate the “i.e.” and “e.g.” from what follows, just as a comma would be used with “that is” or “for example”.
  • Some students use the colloquial phrase “X is where …”, when what they mean is “X is …”. The “where” creeps in in some dialects of English to serve as a way of holding the floor while you think how to finish the sentence—it doesn’t really belong in formal technical writing.
  • “First”, “second”, and “last” are already adverbs.  They don’t need (and can’t really take) an “-ly” suffix. It grates on me the way same way that “nextly” does. “Next” has exactly the same dual status as an adjective and an adverb, but for some reason does not often suffer the indignity of being draped with a superfluous “-ly”.
  • I recommend that students not use the verb “comprise”, as few use it correctly. You can say that “x, y, and z compose A”, “A is composed of x, y, and z”, or “A comprises x, y, and z”. The construction “is comprised of” is strongly frowned on by most grammarists—avoid it completely, and avoid “comprise”, unless its usage comes naturally to you.  “Compose” and “is composed of” are less likely to get you in trouble.
  • “Thus” does not mean “therefore”—”thus” means “in this manner”. Note that “thus” is an adverb, so there is no “thusly”.
  • “Amount” is used for uncountable nouns (like “information”), while “number” is used for countable nouns (like “cells”). There are many distinctions in English that depend on whether a noun is countable or not (the use of articles, the use of plural, “many” vs. “much”), but “number” vs. “amount” seems to be the one that causes senior thesis writers the most difficulty.

2015 January 18

Senior thesis pet peeves

Filed under: Uncategorized — gasstationwithoutpumps @ 19:47
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Every week in my senior thesis writing class, I go over some of the things I saw in student writing that I think need to be fixed.  I’ve decided to try to collect some of the notes here, though I doubt that I’ll ever get a full set, since a lot of the talk is extemporaneous or prompted by questions.  They are not in any particular order.

  • One of the first things I tell students about the structure of a thesis, is that it must start with a clear statement of the research question or design goal of the thesis. (This is traditionally called the “thesis statement,” but I don’t use that term.)  Without explicit demands to put the statement in the first paragraph, and (if possible) the first sentence, students tend to write pages of background material before getting to the point of their thesis. In journalism, this mistake is called “burying the lede”, and it is just as serious a problem in a thesis or thesis proposal as it is in a newspaper article.

    Even after getting this instruction, a lot of students want to write about the overall goals of the lab they are working in, rather than giving the specific goal of their thesis. It sometimes takes two or three iterations before students get a clear, correct statement of the research question or engineering design goal that they are addressing in their thesis.

  • One pervasive problem (often encouraged by the students’ research mentors) is to write the entire thesis in the passive voice. Writing journal articles in passive voice is fairly common, and some people have gotten the mistaken notion that passive is somehow more formal and correct than active voice. But passive is wholly inappropriate for a thesis.The point of a thesis is to establish the research skills of the person writing the thesis. So most of the thesis should be written in first-person singular: I developed a new protocol … ; I transfected the cells … ; I analyzed the data … ; I hypothesize that …  Plural is strongly discouraged—”we” should only be used where other people are explicitly called out by name. Passive voice, which amounts to an assertion that the actor is unknown or unimportant should be avoided.

    I don’t want to prohibit passive voice, though, as there is an important use for it in technical writing, even in theses. That use is inverting sentences, to put the object before the subject: “X did Y” ➜ “Y was done by X”. This reordering can be very useful for improving flow, which relies on putting the old information at the beginning of a sentence and the new information at the end of the sentence.

  • Students often borrow figures from lab mates or from published papers to put in their theses, particularly in the background section. I’d like students to create their own figures as much as possible, but there are plenty of times when copying a figure is the right thing to do. What students usually miss, however, is the need to put an explicit figure credit at the end of the figure caption—something of the form “Figure copied from Smith and Ng [Smith and Ng, 1999]”. A simple citation is not enough, just as a citation is not sufficient defense against plagiarism for copied text, unless there are explicit markings indicating a direct quotation.  When a figure is redrawn or modified, the figure credit should have the form “Figure adapted from …”, rather than “Figure copied from …”, but the explicit credit is still needed.

    One reason I object to copied figures is that students usually do a very bad job of it, copying a low-resolution image off the internet, often with screen-capture tools, so that the image in their thesis is blurry or jagged. Going to the original articles and extracting the PDF images would eliminate at least a little of the awfulness of the copies.

  • Speaking of citations, students often ask what citation format they need to use for their theses. There aren’t any standards for senior theses at our campus, but there are for PhD theses, so I suggest using that style. The PhD thesis citation style on our campus calls for parenthesized author and year format: (Smith and Ng, 1999). That style, though rather long-winded, has the advantage of not requiring the reader to keep flipping to the reference list to see what the citation refers to (a huge advantage in the days of microfilm, but slightly less important now).

    The citation list itself can be in any standard format—I prefer to have the list sorted alphabetically be author and using the full author names, article titles, full journal names, and URLs and DOIs when available. Many journals use a much terser style to save space, but having the full information is useful to scholars, as it provides some redundancy to help correct for typos in the citation.

  • I have to tell a number of students about the concepts of paragraphs and making the first sentence of each paragraph be a topic sentence. Many of the students otherwise start stream-of-consciousness dumps of ideas that go on for pages with no internal structure. Stream of consciousness may have worked for James Joyce (I wouldn’t know, as I could never read more than a page or two of his stuff), but it doesn’t work for scientific writing. Every sentence of a paragraph should be supporting or amplifying the topic sentence.
  • Students often have trouble with vague antecedents for their pronouns—particularly when they use “this” as a pronoun. I strongly suggest that they check every “this” and “that” in their writing, and if it is used as a pronoun, replace it with a noun phrase: “this technique”, “this method”, “this protein”, … Where they can’t find the appropriate noun to use, their readers certainly won’t be able to figure out the intended antecedent. Incidentally, this usage of “this” is referred to as a demonstrative adjective, though it might be more useful to refer to it as an article (like “the” or “an”), since that is the position in the noun phrase that it occupies.
  • A lot of what I tell students has to do with typography and copy editing, rather than with writing per se. For example, I tell them about the 4 types of dashes:
    hyphen –
    a very short mark used inside compound words, to turn a noun phrase into a modifier of another noun, or to mark the end of a line where the word continues onto the next line.
    en-dash –
    a somewhat wider mark (about the width of a lower-case “n”) that is used to represent ranges, such as 1–10 or Jan–Jul.
    em-dash —
    a much wider mark, used for sentence-level punctuation—somewhat like a semicolon or parentheses
    a minus sign –
    used only in mathematics, the minus sign is usually the same size as the en-dash, but has different spacing rules. The text marks (hyphen, en-dash, and em-dash) have no space around them (though some typographers will put thin spaces around em-dashes), but the minus sign has the same spacing rules as the plus sign (with different rules depending whether it represents a unary or binary operator). Basically, if you are not an expert in math typography, you should use LaTeX to typeset your math and trust it to do a better job than you can.

    While I’m on the subject of hyphens, I usually tell students that when they use a noun phrase to modify another noun, they should hyphenate the whole modifying noun phrase. For example, the process of synthesizing amino acids is called amino-acid synthesis, and the pathway that does it is the amino-acid-synthesis pathway.

  • A lot of biology acronyms and gene names are case-sensitive and start with lower-case letters (like tRNA, siRNA, dsDNA, p53, … ). Sentences should not be started with uncapitalizable symbols. If you need to start a sentence with “p53”, try “Tumor suppressor p53” instead. Sometimes just adding an article helps: “tRNA genes” ➜ “The tRNA genes”.
  • Biology papers have two major uses for italics: for new jargon terms in the context where they are first defined and for genus-species names (like Escherichia coli or C. elegans). The genus-species typesetting rules are a bit complicated —genus is capitalized, but species is not; genus can be abbreviated to a single letter with a period, if unambiguous; subspecies or strain names are not italicized. Italicizing words when they are first defined is a simpler concept, one which can be applied to almost any academic writing.
  • There a few words that I object to also. Perhaps the most common problem is the ugly neologism “utilize”, which is used far too often by students, when what they mean is “use”. (The older meaning of “utilize”—to make useful—has disappeared.

2014 October 2

On senior theses

Filed under: Uncategorized — gasstationwithoutpumps @ 10:07
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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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