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Entomological Dissertation Guide, UC Berkeley

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Template:ESO diss guide wiki

ADVICE FOR PREPARING & FILING YOUR DISSERTATION IN ESPM, UC BERKELEY

Version 1.0.3 Pre-wiki version Created 2006-2007


TO THE USERS OF THIS DOCUMENT

This is meant to be a living document. Any ESO members who have filed, are filing, or have unsuccessfully tried to file a dissertation, are welcome to contribute. Anybody else, it's a wiki, we can't really stop you, but seriously, what's your beef?

The goal is for readers to turn in a dissertation to committee members who sign off with smiles and handshakes, not scowls or sighs.


DEALING WITH COMMITTEES

Give your committee plenty of time to read and comment on your work. That stuff about give them a “draft” of the whole thing a month or two early, that they put on the grad division calendar, really depends on the preferences of the committee members. For some members, you might get one chapter back in that amount of time. Talk to former students in the lab who have had the same committee member and see how it all floats. Some committee members will want the piecemeal chapter by chapter, while some will want the whole document at the end, all at once.

One guideline is to allow a month per chapter, with 2-3 weeks at the end for you to proof, format, print, and clean up your lab bench, etc, though this can take longer depending on how good you are with formatting in Word. For a standard 3-chapter-or-so thesis, this takes about 1 semester. At least the semester before you attend the dissertation review process with your committee members, personally speak with each of them to get their assessment of manageable timetables, and to learn of any potential scheduling difficulties. A good strategy is to write chapters as you go, if this is possible for your research.

Key items to consider: Find out if your members prefer electronic or hard copies, give them the format they want. Be prepared to print everything out for some.

Do not assume a short chapter will get read any faster than a long one. Make a point of confirming estimated turn-around times when you deliver material for review. This is primarily a mechanism to prompt the committee member to consider the task in terms of their immediate schedule: it is not a means of obtaining guarantees.

It takes you dropping the chapter off, and you calling on the phone or emailing with reminders that you need to pick up, to get them read.

Phone or brief office visits can be more effective; email is easier to disregard/put off, than when you have somebody live you can pin down for an appointment.

Make sure your committee members will be able to sign the signature page and return it to you [in the U.S.] when you will need their signatures. Also, if a committee member leaves Berkeley permanently for another university, you have one semester or six months (depending on who you talk to) to finish your thesis or you will need to find another member or petition.

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FORMATTING, PITFALLS AND TIPS

  • Absolutely read the dissertation formating guidelines from the Grad Division-multiple times.
  • It is possible to use LaTeX to format your dissertation, and there are various document classes available to assist with this (search the UCB website for “latex thesis” to see several people’s recommendations). However, unless you love LaTeX, or unless your dissertation will include formulae that are difficult to format properly in ‘ordinary’ word processing packages, don’t use it.
  • Set your computer’s default margins to “dissertation margins” so any new M.S. Word file you start is dissertation style—left 1.5”, bottom 1”, top 1”, right 1”. MS Word’s word-wrapping sometimes lets things exceed the right margin slightly, a right margin of 1.2” may be safer. It is better to include extra buffering space, because certain printers will actually differ in margin width, so you want to be sure. I have not met anyone who has had grad division actually measure the margins (they typically do a quick flip through, and nothing more) but you don't want to be the first.
  • Page Numbering: MS Word’s default “footer” is only ½”, you will need to extend it to ¾” or more to get the page numbers to sit the minimum distance (3/4”) from the edge of the paper. This means that the BOTTOM of the number must be 3/4" from the bottom of the page, not the center of the number. This is kinda tricky to do—you use the page setup button on the header/footer menu to get to the header/footer size box, which is then a tab click or two from the page-setup box. If you have merged documents, you will need to make sure it applies these settings to “all sections”, otherwise there will still be inconsistencies in the page number positions. Centering the numbers is recommended so that when someone prints it double-sided it will look correct.
  • Color figures: these need to be changed to grayscale, and some don’t look so great upon switching. Make sure you like your figs without color, or reformat them for better b/w contrast. If you’re feeling frisky, you can pull these into Photoshop and manually adjust the contrast of the black and white image. Your best bet is to stick with colors recommended for color blind presentation, as these look good in color and grayscale.
  • Number your pages, at least provisionally, in the chapters you give your committees even if these will change later. If your member drops his/her copy and the binder clip comes off, it’s a problem to reassemble it w/o page numbers. Keep track of changes in page numbers as well, and update in your TOC.
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  • The exceptions are the title page, the copyright page, and the signatures page. Look at the guidelines for these as they need to match exactly.
  • Chapters are often kept in multiple Word docs, so formatting can be a pain to align across all of those documents, especially if some of them have been completed in different reference formats for various journal submissions. Many people prefer not to keep the whole dissertation in one single document, so it helps to have a checklist to go over with each chapter so you can make everything consistent. Related to this, it is a good idea to refer to your dissertation chapters, rather than any resulting published articles, for self-cites in later chapters.
  • Examples of potential formatting checklist items:
  • 12 pt double spaced for text
  • Margins L1.5", others 1"
  • Page numbers 3/4" from bottom
  • Indent Paragraphs
  • Check references format
  • Check section title format consistency
  • Chapter title separator page
  • Figures and Tables
  • Figure and table labels consistent throughout, e.g. 2.2, 3.1
  • 10 pt font for big tables (can be even smaller for huge tables, but 10 is recommended)
  • Placeholder numbered pages for elongate figures and tables (see below)
  • Double space for figure and table captions
  • Figure and table legends with page numbers in table of contents

You might want to format this as a table with a checkbox for each item/chapter combination, as well as checkboxes for the intro and conclusion.

  • MS Word does not automatically format boxes surrounding tables within the margins, you may need to “shrink” them manually to get them to fit the margins. You can do this by going into the properties tab of the graph and change the scaling to 80%, 50%, whatever it takes to get it within the margins.
  • “Landscape” type figures/tables. The page numbering on these can be a pain. On some printers, the best procedure was as follows:
    • 1. Print out blank pages with the correctly formatted page numbers for the figs/tables or put placeholder blank pages where your figure should be so that the page numbering stays correct for figures in the correct order.
    • 2. Put them back in the tray (number side down, number toward the “back” or inside of the printer tray, some printers). You may need to test this with some scrap paper first to make sure everything fits correctly.
    • 3. Print your figures (without pages numbers) onto the pre-numbered pages.
    • 4. Swear, crumple paper, and try again with the paper inserted the other way.

(jdl notes: do not waste two days trying to get Acrobat to put page numbers in the proper place for landscape tables like I did, it is tricky and the above methods is easiest, though it limits your ability to file electronically).

FILING

The dissertation preparation guide from the grad division is the most helpful thing for the actual filing process. The people working in 302 Sproul can also help you. Additional things not in that document...

The fancy paper you need (see dissertation guide) costs about $28-50 for 500 sheets. Assuming you will blow up the first copy or two of your diss, and your magnum opus is between 100 and 300 pages, you’re going to need two reams, minimum. Some stores will allow you to return unopened reams of paper if you keep the receipt. If you are lucky enough not to have to break into the backup paper, you can get some money back and buy some booze instead. If you have a systematic monograph that’s 1000+ pages long, then God bless you, and I think they have emergency loans available in financial aid.

Check out the lab’s print supplies about a week before you are going to start your printing marathon. Make sure all toners, and regular paper are going to last when you need them to. Printing a “supplies page” or “consumables page” should tell you, hopefully accurately, how much of each thing is left. Talk to the lab manager if it looks like you’re gonna run out of anything, and order more. Some of the stuff (toners for the B/W duplex printer, for instance) are available on-demand in the chem stock room, or the Life Science Annex stockroom.

You can order hardbound copies for about $35 each (minimum 3, what a nice gift for Mom) from Proquest, so you don’t need to do your own at Copy Central or Kinkos. But, you can, it might save a few bucks.

Proquest has versions that are 2/3rds of the original size and print double-sided, which can be good given the mandatory double-spacing that applies to most of the text. However, if you want a nice one for your shelf, they’re not the prettiest; both the shrinkage and shift to grayscale in the Proquest ones can uglify your work. There are binderies and printing companies that offer more varied products (full or reduced size, different cover and title embossing styles, custom or University-matching logos/colors, customized content, etc.). Some binderies also do floppy-covered bound copies that cost between $5-10 each, which can be good if you want to leave copies with the lab or give them to people you’d like to thank. Make sure you at least ask your committee members if they would like a bound copy. Most will say no (thankfully), but you should still always give one to your adviser (preferably with a nice little note saying how great they were on the title page).

Grad Division Staff will help you, at least by giving you a thumbs up/thumbs down on your formatting before you go to officially file. You should definitely take a final draft copy of your dissertation on plain copy paper in and have the staff check it over before you do the “big print” if you’d like to check before you spend the big money. The staff consider this a regular part of their jobs and takes a load of stress off for the final print.

If you go with a not-acceptable dissertation (page numbers wrong, margins wrong, whatever)... they’ll send you back to the lab and tell you to come back with it done right; this happens all the time! So it might not be best to show up at grad division on 3:45 on the last Friday of semester when you’re not sure it’s absolutely flawless.

    • Copyright Issues: Note that this paragraph is in no way written by a lawyer or anything, and should not be used as legal advice in any way, but is merely here to remind readers of a potential concern and to point out one ex graduate student's probable misunderstanding of something complicated. The reader is advised to discuss this issue with their PI, dean's office, Grad Division or someone with an actual law degree for details. The issues relating to dissertations, publication, and copyright are fuzzy to be sure and universities, journals, etc are beginning to make students aware of the issue. First of all you should include a copyright page in your thesis (see the Grad Division Guidelines). Do not, however, on advice of one of the women who checks the dissertations, waste the money to have Proquest actually register it for you with the Library of Congress unless you are going to be publishing it as a book or whatever and you expect to turn a profit. However, there is an issue of copyright when you have submitted chapters for publication. Technically printing of the dissertation and putting it on the library's shelf constitutes publication. If a chapter/figures/tables have been previously published this could (read maybe possibly in a million years COULD, like maybe if you cure cancer somewhere in there or solve global warming or something) become an issue. If you want to be fully on the up and up you a) have to obtain written permission from coauthors (and by written, this means on actual paper, with an actual ink signature; no emails will suffice for this) on any chapter that has been published and b) have to obtain permission from the journal to use the material in your dissertation, and c) submit all of this to the dean 1 month prior to filing.
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OTHER STUFF

Genbank accession numbers: You should include these in your manuscript if you’ve used molecular data, and your advisor believes it is appropriate, pre-journal publication. Some advisors have requested withholding of this data until journal acceptance. If you’ve never done it before, give yourself a couple of days to get used to the computer program Sequin, which is not as easy as it should be, which formats your raw data into Genbank format, and a couple more days to get a response from NCBI re: your accession #s.

Voucher specimens: Don’t forget to deposit your voucher specimen into an appropriate museum. It’s easy to forget to do this once you’re done, but it’s a pretty important part of the greater scientific process, even if the graduate office doesn't care.

Filing fee: If you are filing in the summer, you’ll need to go on filing fee for the fall. Even though this is in summer, your degree will still say Fall 200X. During the regular semester, you can just stroll on into the filing office, plop your dissertation down, and graduate. If it is summer, and you need to file, you need to first submit the paperwork, pay your CARS bill, and then file.

This is not a fast process—allow 2-3 weeks for the following to happen: 1. Find Richard Battrick and fill out the filing fee paperwork. It requires his signature and then needs to be turned in to the grad division. 2. Wait for a letter to come in the mail from the dean saying you have been accepted for filing fee. (~1 week). 3. Wait for someone to push a button to charge the filing fee to your cars account (~1 week or more). 4. Pay the filing fee online or at University Hall (~$200) 5. Go in and file.

Diplomas and certificate of completion: Say you have a job that you want to start, and they need to know you have graduated. When you graduate, you don’t get your diploma right away, and better yet, if you file in the summer, you won’t be seeing your diploma until about December or later. Luckily, when you file, you actually get what is called a “Certificate of completion”. This handy document is proof that you have finished everything you need to finish to graduate, and it’s as good as the diploma for job purposes. You can also look forward to a lollipop (mocha!), a sense of accomplishment, and a bleak future where you are either over- or under-qualified for almost every job. CONGRATS!

  • Oh, man. It was mocha flavored? I immediately lost mine at Red Rock 45 minutes post-filing, before getting to eat it.

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