Physics & Astronomy Graduate Students (PAGS)

Writing a JHU thesis

Introduction
JHU requirements
Thesis template
Writing your thesis
Helpful hints
Thesis defense
Turning in your thesis

Introduction

There's already a great JHU thesis page in existence, from a former Astro PAGS named Charles Danforth:

Charles Danforth's thesis page now hosted here

Because this is such a great reference, I'm going to focus more on how to get started on a generic thesis and how to actually turn IN your thesis, which is important but often overlooked.

JHU requirements

The best place to start is probably the Sheridan library's thesis guidelines page:

Sheridan thesis guidelines page

This has all the university thesis requirements (which are all taken care of for you in the LaTeX template I point you to next). It also has information about copyrights; what constitutes copyrighted material, when you can use such material freely, and when you should get permission to use such material. Most people probably won't need this (I didn't) but if it does apply to you, make sure you get signed permission letters before you go to turn in your thesis.

Thesis template

You should expect to be using LaTeX, so learn it early and learn it well. Being familiar with LaTeX before you start your thesis will make your life much, much easier. A previous Hopkins grad updated all the university's LaTeX template files in 2005; I used these files out-of-the-box, and they conformed to every requirement. You can find all these files on the library's LaTeX page:

Sheridan thesis LaTeX page

The important files are:

thesis.cls: This is the file where all the style definitions are set to conform to JHU requirements. It takes care of formatting your chapter/section titles, your captions, you name it. You shouldn't have to edit anything in this file, unless the university changes requirements.
jhuxx.clo: Where 'xx' = 10, 11, or 12. The number corresponds to font size (I used 12). The font size is an input to thesis.cls, which then uses the corresponding .clo file.

You can download all of the files on this page and try running their root.tex to produce the sample output file. All files should be in the same directory (mine is oh-so-cleverly titled THESIS/).

Writing your thesis

Actually, here I'm going to refer back to Charles' thesis page. His "Writing Your Thesis in Eight Easy Steps" section defines pretty much everything you need to know. For some extra examples, here are some texcerpts from my own thesis:

thesis.tex: My main file. As Charles also recommends, I put every chapter in a different tex file, and then just input them all into this main file, which keeps the main file small and manageable. Actually, I'm a little more obsessive-compulsive than that; if you look through my script you'll see I gave every chapter its own directory too!
latps: The c-shell script I used to compile my thesis as a postsript file. Since my main file is thesis.tex, I would run this script with the command "./latps thesis", and it would produce an output file thesis.ps. You can see it's a really simple script, just runs pslatex and then converts the .dvi to a .ps using a few options that make the eventual conversion to pdf a little nicer. You usually have to run it twice to get the internal refernces correct.
ps2pdf.csh: And the c-shell script I used to convert the ps to a pdf. It takes care of getting all the fonts embedded and properly converted and sized, etc etc. You run it with "./ps2pdf.csh", as long as your postscript file is titled thesis.ps. If yours has a different name, just edit ps2pdf.csh. You could combine this script with latps... but generating the pdf takes a while when your file is large. I prefer to work off the ps, and only generate the pdf when I need it.

Helpful hints

Writing your thesis is, of course, up to you, but I have a few little tips that made life easier for me.

Draft version

When you setup the document in your thesis (with the \documentclass command) you have several options. The final thesis has to be single-sided and double-spaced, but that might not be optimal while editing. I used the "draft" input instead of "thesis" while editing, so that everything would be single-spaced.

New commands

In my "thesis.tex" file, you also see as an input a file called "defs.tex." The "defs.tex" file has a whole list of symbols that I defined for things I used frequently. For example, in particle physics mass is defined in units of eV/c^2. Rather than write out GeV/$c^2$ in my tex all the time, I put this line in my defs.tex:

\newcommand{\gevcc}{\ifmmode \rm{GeV}/c^2%
                 \else%
                           \mbox{GeV}$/c^2$%
                 \fi%
                 }%

Now this command is defined whether or not you're in math mode, so I could use $10~\gevcc$ or 10 \gevcc and it would Tex the same way. This is another way to keep your Tex easy to read, by putting all definitions in one place. Defining easy-to-type commands for hard-to-type Tex that you use frequently will also help your thesis writing go faster!

Tables and figures

The JHU guidelines page doesn't give you much guidance on requirements for tables and figures. I put my figure captions below the figures, and my table captions above the tables, since this is the standard in high energy physics publications. For my table style, I used no vertical lines, like the following:

\begin{table}
\begin{center}
\parbox{0.8\linewidth}{
\caption[Standard Model force carriers]
	{The four forces in nature and their corresponding gauge
	bosons.  The strength roughly gives the relative magnitudes 
	of each force in the case where two protons are just in 
	contact~\cite{perkins}.  Masses are taken from Ref.~\cite{pdg},
	where the gluon mass is a theoretical value.}
\label{tab:forces}}
\begin{tabular}{llccc}
\hline 
Force & Mediator & $J^P$ & Mass (\gevcc) & Relative Strength \\
\hline\hline
Strong Nuclear	& Gluon ($g$)	& $1^-$ 	& 0	& $1$        \\
Electromagnetic	& Photon ($\gamma$) & $1^-$ & $< 6~\times10^{-17}$ eV/c$^2$ & $10^{-2}$  \\
Weak Nuclear	& Charged: $W^{\pm}$ & $1^-$ & $80.403\pm0.029$ & $10^{-7}$  \\
		& Neutral: $Z^0$ & $1^+$ & $91.1876\pm0.0021$ &  \\
Gravity		& Graviton  	& $2^+$		& unobserved & $10^{-39}$ \\
\hline
\end{tabular}
\end{center}
\end{table}

Another tip -- your table and figure captions will appear in your lists of tables and figures in the front matter of your thesis. If you define a caption as \caption{blah blah blah}, then ALL of "blah blah blah" will appear both in your caption and your list. If you instead define a caption as \caption[BLAH]{blah blah blah}, then "blah blah blah" will appear as your figure caption and "BLAH" will appear in your list. So you can make your figure captions as long as you like, but I tried to make all the captions in my list of tables/figures only one line long.

Thesis defense

Instructions for your thesis defense are on the PHA website:

PHA thesis page

It usually only takes a couple of weeks to set up a thesis defense. You're supposed to provide a copy of your thesis to all your committee members at least two weeks before the defense. Since I was based at Fermilab, I emailed the pdf to my committee members, and they all printed it out themselves. If you're based at Hopkins, you might be able to just email them the pdf, or you might be required to deliver them each a paper copy, I don't know that part.

For my defense, the two professors in my field actually read the thesis and gave me editorial comments. After the defense was over, I spent some time going over my thesis and addressing their comments before I actually turned the thesis in.

Turning in your thesis

Once again, instructions are on the Sheridan library webpage:

Sheridan dissertation submission

You are responsible for all fees to turn in your thesis. You are also required to get at least two extra copies made -- one for the physics dept. reading room, and one for your advisor. The library won't accept electronic submissions, you have to actually print out three copies of your thesis (single-sided, double-spaced) on ACID-FREE paper and physically transport them to the library. They will deliver the two extra copies to the physics dept. for you after they're bound. They will NOT mail extra copies off campus, you have to pick those up at the library.

ProQuest UMI publishing

All dissertations will be published by ProQuest UMI. You should print out and read through the publishing agreement which is available on the above webpage. When you turn in your thesis, you have to turn in the publishing form on pp 3-4 of this manuscript. You have two basic options with the publishing:

Open Access means the thesis will be available on the internet for free to anyone who wants it. Currently this is NOT required, and it costs an extra $95.
Traditional means someone would have to pay a fee to access your thesis. This option does not cost you anything extra.

I chose traditional publishing, since I already know that my thesis will be posted online by Fermilab and freely available to the public there. You also have the choice of having UMI register your copyright (again, for an extra fee, currently $65). There's a section of the publishing agreement which explains why you might want to do this (I didn't). You could also buy extra copies of your dissertation through UMI, but it's cheaper to get them through the Sheridan library.

ProQuest will accept either a paper or electronic copy of a thesis to be published. JHU is still doing it the paper way; they take the bound copy of your thesis that will stay in the library and send it to ProQuest. ProQuest makes their own copy and sends the bound copy back to the library. I asked if it would be possible to turn in an electronic copy for ProQuest, and was told that it is possible. When you turn in all the paper copies of your thesis, also turn in a disk with the pdf of your thesis on it and they'll send that to ProQuest instead of the paper copy. I didn't actually try it though.