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thesis_lore [2012/06/01 18:58] – [Filing in the Summer] nmccthesis_lore [2017/08/04 22:31] (current) – [Filing in the Summer] dyas
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 +======Thesis Lore======
 +
 +The [[http://grad.berkeley.edu/academic-progress/dissertation/|Dissertation Guide]] lists the various rules for building and submitting a dissertation, so start there.  The [[filing timeline]] is also very handy.
 +
 +======Advancing to Candidacy======
 +
 +When you advance to candidacy after your qual you can drop one of your qual committee members (you only need 3 for your dissertation), but you cannot drop your outside member, or your adviser (who is your dissertation chair).  Check the grad student handbook (above link) for details on who can and cannot serve on your committee.  It is also relatively easy to change your dissertation committee at any point after your qual, just use [[http://grad.berkeley.edu/policies/pdf/Recon.pdf|this form]].
 +
 +
 +=====The Stapler Dissertation=====
 +If you have published papers, you can probably put together a "stapler dissertation".  The papers do not have to be on the same topic and you do not have to re-work them into a coherent whole.  Just write a several-page introduction giving the appropriate background and references to demonstrate your understanding of how your papers fit into larger fields and then change the "title" of each paper into a "chapter".  That is a bit oversimplified, but really, you do not need a single, over-arching "thesis" with a big conclusion at the end.  Published papers are //prima facie// evidence of doctoral-level competence, and if you have enough of them to make a dissertation, you are (nearly) finished.  It also does not matter what you said you would do at your qual.  Your committee will not care (or remember).
 +
 +=====What the heck is "Filing Fee"?=====
 +
 +"Filing Fee Status" is a special kind of university registration which lets you file your dissertation sometime during a semester, but leaves you effectively unregistered in all other ways. Notably, you lose many regular student privileges such as Class Pass, use of the gym, and health insurance (but note that your spring SHIP insurance and Class Pass are good through most of the summer, until ~August 15, even if you are approved for filing fee status before that date).  Then why would someone ever want to do filing fee? It's cheap ($243 as of 2012), far cheaper than registering regularly. 
 +
 +One case in which Filing Fee might be a good idea is if you already have a sweet postdoc lined up somewhere, but do not quite manage to get your dissertation done in time, so that you need to file in the first week of September, or early January or something like that.  Rather than registering for an entire semester just so you can file your dissertation and then leave, you can pay filing fee, file your dissertation, immediately head off to magical postdoc-land. 
 +
 +When on filing fee status you can't be paid as a GSR; you need to get a special appointment like "junior specialist."  Once you actually file you will then have to change your appointment (a hassle) to get paid as a postdoc, if you are sticking around for a while.  You also have to start paying off any undergrad student loans you've deferred. 
 +
 +
 +=====Filing in the Summer=====
 +
 +Since summer 2007, university regulations have required students to register for 3 units in the summer if they want to file their degrees in the summer.  In summer 2012, the cost of 3 units was $1666.
 +
 +There has been past confusion about whether the fall filing fee will cover the preceding summer.  In other words, even if you intend to file during the summer, can you go on filing fee for the fall in order to circumvent the summer course requirement and save your advisor some cash?  Yes, this IS possible, based on discussions with Dexter in Spring, 2014.  If you receive e-mail or word-of-mouth saying otherwise, your safest option is to walk over to the Graduate Degrees office (318 Sproul) and ask them directly.
 +
 +Assuming that fall filing fee is a permitted option for filing a summer thesis, here are the tradeoffs:
 +
 +Registering for summer units:\\
 +- more expensive for your advisor\\
 +- keep GSR status\\
 +- keep SHIP insurance (see below), Class Pass, student gym rate, etc.\\
 +- if you file early in the summer, can get a certificate of completion without waiting for the filing fee to be billed\\
 +- file by August deadline to avoid extra registration (or filing fee) expenses for the fall\\
 +- if you miss the August deadline, you're still a student
 +
 +Fall filing fee:\\
 +- save your advisor ~$1400 (as of 2012)\\
 +- no GSR status, so your advisor will have to set up a Junior Specialist appointment for you (through RES or one of the Astro HR staff)\\
 +- no student privileges over the summer\\
 +- SHIP insurance expires in mid August\\
 +- regardless of when it is approved, the filing fee will not be billed to you until late July\\
 +- you cannot receive a certificate of completion until the filing fee is billed and paid (if you're starting a post-doc, they will likely require this)\\
 +- once on filing fee, the August filing deadline no longer applies\\
 +- file by December deadline or you must re-apply for admission to the university
 +
 +**For international students:** if you want to use OPT, then you need a new I-20 F1-OPT and employment authorization (EAD) card to work in the US. The starting date of the EAD card depends on your program end date. The rules may be tricky and change over time. Please consult to the Berkeley International Office before making decision of finishing in the Summer or Fall semester.
 +
 +
 +===== Health Insurance Post-Filing ====
 +
 +Health insurance may be the last thing you want to worry about when trying to finish your dissertation. Luckily, you probably do not have to: Spring semester health insurance extends through August 14, regardless of when you file, so you are covered after you graduate. Fall term insurance extends through January 14. See [[http://uhs.berkeley.edu/students/insurance/aftergraduation.shtml| this page at UHS]].
 +
 +If you want to buy SHIP insurance while on filing fee after SHIP expires, you can purchase it for one extra semester; it's just under $2,500 (as of 2014). 
 +
 +======LaTeXing Your Dissertation======
 +
 +To get a bomb of all the files you need to start LaTeXing your dissertation,
 +use [[https://github.com/pkgw/ucastrothesis|the ucastrothesis Git repository]] created
 +by Peter Williams. You don't need to know how to use Git to use this: [[https://github.com/pkgw/ucastrothesis/zipball/master|this link]] will give you a Zip of the most recent version, for instance. (Although Peter suggests that you both learn [[http://git-scm.com/|Git]] and use it to version-control your thesis!) You can then follow the directions in that repository
 +and start reading the main files to figure out how the pieces fit together.
 +
 +Old instructions for getting the LaTeX files are farther below.
 +
 +====Margins====
 +
 +They will reject your dissertation if it does not have the right margins.  The limits are 1 inch all around, and the page number must be no closer than 3/4 inch from the edge (and consistently placed and on every single page, even chapter pages).  These are minimums, so you cannot go wrong if you give yourself some buffer room.
 +
 +Don't use the "twoside" option in the ucthesis style for your submitted version. The Dissertation Guidelines state that page numbers should be in a "consistent" location in your dissertation, but since the move to electronically submitted theses, this location is what you see scanning through the PDF, **not** what you'd get printing out the thesis with a duplexing printer. The "twoside" option makes things look nicer if you're going to be printing the PDF out yourself on a capable printer, though.
 +
 +If you run into problems with your margins, tweak the options given to the "geometry" package. The "showframe" option prints out the margins it's using making it relatively easy to spot overflows -- though this option only works on all pages for geometry version >= 5.0. If you are using a Mac with Preview, you can measure the PDF margins by using the "select" tool in conjunction with "show inspector".
 +
 +The most common problems with margins come from formulae, tables, and figures.  Tables and Figures are discussed below.  Check all of your formulae (especially in-line formulae!) and make sure they conform!  You may need to re-format some of them, or shrink the font.
 +
 +====Tables====
 +
 +The deluxetable package sometimes works in theses but breaks down other times, especially for very long tables. Try using the [[http://www.astro.psu.edu/gradinfo/psuthesis/longtable.html|longtable]] package instead.
 +
 +If your tables run wide (which happens a lot with these fat margins) there are a few tricks you can try to get them to fit.  The first is to make your columns closer together with this command:
 +
 +  \setlength{\tabcolsep}{0.05in}
 +
 +Adjust to taste.  If you're really desperate, you can make the columns separation negative
 +
 +   % change
 +   \begin{deluxetable}{l*{14}{r}ccc}
 +   % to
 +   \begin{deluxetable}{@{\extracolsep{-6pt}}l*{14}{r}ccc}
 +   
 +If that's not enough, you can use the pdflscape package and invoke the landscape environment to make your tables landscaped. (Don't use \rotate command.) Here's how a table might begin:
 +
 +  \begin{landscape}
 +  \tiny
 +  \begin{center}
 +  \begin{longtable}{l@{ }rccccccccccr}
 +
 +It's all on the longtable website.  A nice PDF with a description of the longtable package is [[http://www.cs.brown.edu/system/software/latex/doc/longtable.pdf|here]].
 +
 +The downside to using the landscape environment is that you have to put it outside of the floating table environment.  This results in LaTeX putting the table in that exact place relative to the text, meaning you could end up with half the page before the table being empty.  Another alternative, at least for tables that are wide, but short, is to use the "sidewaystable" environment in the "rotating" package. Whether or not this would suffer the same problems as deluxetable when also dealing with very long tables is unknown.
 +
 +
 +====Figures====
 +
 +For figures, make sure your figures are not too big.  If you have played with axes and such you might find the figures are pushing your captions out beyond the margins.  If this happens, the "pdfcrop" tool is great for removing extraneous whitespace. (If you're generating figures from EPS files, you can open up the file in a text editor and play with the line that reads "BoundingBox:" and play with the numbers there.)
 +
 +The default LaTeX effect on figures will be to put large-ish figures on their own page (even when text could easily fit around them on the page) and smaller figures on the top of pages, with text underneath.  Feel free to have all figures take up their own page by making them fill the page:
 +
 +   \includegraphics[width=13cm]{intro/figure1}
 +
 +though this is by no means a requirement.  You can also force your figures to be on a "page of floats" (= no text) in the figure command: 
 +
 +   \begin{figure}[p]
 +
 +Another useful command is in the "afterpage" package; once you have added this package to \usepackage in thesis.tex, you can then use the following command to force a figure to be on its own page:
 +
 +   \afterpage{\clearpage}
 +   \begin{figure}
 +   ...
 +   \end{figure}
 +
 +though again, there is no formal rule requiring a figure to be on its own page.
 +
 +If you have wide figures that you want to have rotated sideways, you could use the landscape environment, but it may not be ideal. The problem is that you have to put it outside of the floating figure environment. This results in LaTeX putting the figure in that exact place relative to the text, meaning you could end up with half the page before the figure being empty.  Another alternative is to use the sidewaysfigure environment in the "rotating" package.
 +
 +====Captions====
 +
 +The captions of your tables and figures will appear in the lists of figures and tables after the table of contents.  If you'd like shorter table and figure (or even chapter!) names, use the optional argument in the caption (or chapter!) command:
 +
 +  \caption[x vs. y]{x, corrected for nonlinear charge 
 +  dispersion as a function of redshift and partial 
 +  ionization vs. y sinh (gamma) (uncorrected for GR 
 +  effects past 4th order)}
 +
 +====Converting Papers====
 +
 +If you're going the stapler route, one of your tasks will be to convert the latex files for your manuscripts into individual chapters of your dissertation.  One potential pitfall is you are likely to have latex labels multiply defined in each of your documents, e.g. having "\section{Introduction}\label{sec:intro}" in more than one chapter.  These multiple definitions can cause the references to be confused when processing your master latex file.  To avoid this problem, Mike Fitzgerald wrote a Python script ({{thesis_lore:convert_chap.py.txt|convert_chap.py}}) to add a prefix to the labels and references in a chapter (e.g. "\label{sec:intro}" -> "\label{vega_sec:intro}").
 +
 +The thesis.tex file gives you the option of including with each chapter an abstract and acknowledgments.  You should not include a list of co-authors or a publication reference; it is //your// dissertation.  (But see below for the forms to fill out for previously published material).
 +
 +====== Filing Your Dissertation ======
 +
 +**Dissertations must now be filed electronically**, thus "saving of approximately half a million pages of paper per year, making Berkeley doctoral dissertations more widely accessible, and sparing doctoral candidates the cost of purchasing archival-quality paper."
 +
 +The filing must be done online four business days before the end of the semester.  Once you receive a confirmation email from the Degrees Office, you will need to bring them hard copies of the required documentation: two surveys, a release form, and the approval page signed by your committee.  None of these documents needs to be on archival paper.
 +
 +If your dissertation contains previously published material, you will need to obtain a signed letter from your committee chair (adviser) stating that this constitutes dissertation-level work.  You will also need a letter from every co-author stating that it is okay for you to reproduce this material in your dissertation.  Alternatively, a printed email from each co-author stating the same thing can be included with the application, sent to Graduate Services along with copies of the published material.  If you have a very large number of co-authors, a letter from your adviser to the dean stating that this requirement is a hardship for you since all of the many co-authors can not be reached and that your adviser speaks for all of them in approving the use of this material may be sufficient.  This has worked in at least one case (Dexter has a copy of the letter that worked in her records), but it has also been known to fail, so if you want to try this, start several months in advance.
 +
 +====== Old LaTeX File Links ======
 +
 +(Peter Williams suggests you check out the ucastrothesis files mentioned above rather than these, but here's the info for posterity.) You will need the following files in your latex directory (on a Mac, it's often ~/Library/texmf/tex/latex/misc/ -- if that directory doesn't exist, you can make it) or main thesis directory:
 +  * {{thesis_lore:ucthesis.cls.txt|ucthesis.cls}}
 +  * {{thesis_lore:tweak_ucthesis.sty.new.txt|tweak_ucthesis.sty}}
 +  * {{thesis_lore:bibsetup.sty.txt|bibsetup.sty}}
 +  * {{thesis_lore:aasmacros.tex.txt|aasmacros.tex}}
 +  * [[http://nuclear.ucdavis.edu/~rpicha/sample/|the uct1x.clo and uct1x.sty]] files, where x={0,1,2} -- if this has moved, google the file names.
 +
 +Chop off the ".txt" (and ".new") at the ends of these filenames.  Then, use this {{thesis_lore:thesis.tex.txt|thesis.tex}} file as a template for the overall thesis document, which uses the UC Thesis environment and imports individual chapter tex documents from appropriate subfolders.  Modify this {{thesis_lore:frontmatter.tex.txt|frontmatter.tex}} file to make your appropriate preliminary pages.  Use this {{thesis_lore:topic.tex.txt|topic.tex}} file as a template for individual chapter files (and put it in a folder called "topic").  Also, use this {{thesis_lore:approvalpage.tex.txt|approvalpage.tex}} file as a template for your dissertation approval page, which your committee signs.  These files should have enough stuff to make typesetting your thesis possible without having to learn too much of the guts of LaTeX.
 +
 +If you have two co-chairs, then some of the files need to be altered to note this.  In this case, use these modified versions of {{thesis_lore:ucthesis.cls.cochairs.txt|ucthesis.cls}}, {{thesis_lore:tweak_ucthesis.sty.cochairs.txt|tweak_ucthesis.sty}}, and {{thesis_lore:frontmatter.tex.cochairs.txt|frontmatter.tex}}. Just cut the ".cochairs.txt" off the filenames.
 +
 +tweak_ucthesis.sty is the one that sets the margins.  Warning: the newest version of TeXShop for Macs is currently off on the left hand margin by 1mm.  You'll need to change the textwidth, etc... in this file if you find you are having this problem.
 +
 +The margins set up in the above files should be correct (they have been accepted for at least two dissertations as of May 2010).  If for some reason you want/need to tweak your margins, there is a command in ucthesis.cls, for instance, which reads "\topmargin xxxxin" where xxxx is some number of inches for the top column -- change that until you have at least 1 inch.  If you are using a Mac with Preview, you can measure the PDF margins by using the "select" tool in conjunction with "show inspector".
  

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