Thesis in a Box

by

Mark Andrew Paskin

B.A. Hon. (Cornell University) 1998M.S. (University of California, Berkeley) 2000

A dissertation submitted in partial satisfactionof the requirements for the degree of

Doctor of Philosophy

in

Computer Science

in the

GRADUATE DIVISION

of the

UNIVERSITY OF CALIFORNIA, BERKELEY

Committee in charge:

Professor Moe Howard, ChairProfessor Curly Howard

Professor Larry Pine

Fall 2004

The dissertation of Mark Andrew Paskin is approved:

Professor Moe Howard, Chair Date

Professor Curly Howard Date

Professor Larry Pine Date

University of California, Berkeley

Fall 2004

Thesis in a Box

Copyright c© 2004

by

Mark Andrew Paskin

Abstract

Thesis in a Box

by

Mark Andrew Paskin

Doctor of Philosophy in Computer Science

University of California, Berkeley

Professor Moe Howard, Chair

Thesis in a Box is a framework for easily using LATEX to create a PDF doctoral

dissertation that obeys the formatting requirements of the University of California,

Berkeley.

Professor Moe Howard, Chair Date

1

Acknowledgements

I would like to thank Kevin Murphy, who inspired (and contributed to) this project

by publishing the LATEX source of his dissertation [Murphy, 2002].

i

Dedicated to the Open Source Movement

ii

Contents

1 Introduction 1

1.1 What is Thesis in a Box? . . . . . . . . . . . . . . . . . . . . . . . . 1

1.2 Why use PDF instead of PostScript? . . . . . . . . . . . . . . . . . . 1

1.3 Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.4 Outline of this thesis . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Appendix 1.A How to make an appendix . . . . . . . . . . . . . . . . . . 4

2 Files 5

3 Compiling your thesis 7

4 Conclusion 8

4.1 Contributions of this thesis . . . . . . . . . . . . . . . . . . . . . . . . 8

4.2 Directions for future research . . . . . . . . . . . . . . . . . . . . . . 8

Bibliography 9

iii

Chapter 1

Introduction

1.1 What is Thesis in a Box?

Thesis in a Box is a LATEX framework for formatting a PDF doctoral dissertation at

the University of California, Berkeley.1

1.2 Why use PDF instead of PostScript?

PDF has several advantages over PostScript: in many cases it is more compact;

more people have PDF readers than PostScript readers; and, PDF readers have more

functionality like hyperlinking and annotation.

Thesis in a Box uses the hyperref package and compiles your LATEX source di-

rectly to PDF. This gives your thesis several nice features, which are described below.

1I hope it will be useful to students filing at other schools, but the format may need to be changedto satisfy other school’s requirements.

1

Chapter 1. Introduction

1.2.1 Bookmarks

The first advantage is that, using Adobe Acrobat, the readers of your thesis can

quickly navigate the chapters and sections of your thesis using the bookmark window.

If you are viewing this document in Adobe Acrobat, look on the left hand side and

you will see that you can quickly navigate through this document.

1.2.2 Hyperlinking

The second advantage is that the following types of references are automatically

hyperlinked:

• chapter and section references, including those in the table of contents (e.g., go

to Chapter 2)

• equation references (e.g., check out (4.1))

• citations (e.g., this document is [Paskin, 2003])

• index references (e.g., this boldface item is indexed as “item”—check the index

at the back)

1.2.3 Annotation

PDF files support reader annotation, which can a useful way for your thesis committee

to comment on drafts.

1.2.4 Graphics

Because your thesis is compiled directly to PDF, all graphics you include must be

in PDF format. Thesis in a Box includes the package graphicx, so you can use the

\includegraphics command to include PDF graphics directly into your thesis. If

2

Chapter 1. Introduction

Figure 1.1: A figure. This caption is typeset in sans serif font to distinguish it from bodytext; you can turn this off if you like.

you have used EPS graphics in the past, they can be converted to PDF format using

the Unix utility epstopdf. An example is given in Figure 1.1.

1.3 Contributions

Thesis in a Box is useful for a number of reasons. First, it implements the strict

formatting requirements of the University of California, Berkeley. Second, it gives

you easy examples of how to do things in LATEX that you might not have done before,

like citations, indexing, tables of contents, etc. Finally, Thesis in a Box comes with

a Makefile which makes it really easy to compile your thesis.

1.4 Outline of this thesis

The rest of this document is structured as follows:

• In Chapter 2 we describe the files in the distribution, and what you should (and

should not) change to write your thesis.

• In Chapter 3 we describe how to compile the LATEX thesis into PDF. For a quick

start, you can compile this document by typing make.

3

Chapter 1. Introduction

Appendix 1.A How to make an appendix

Using the appendix package, you can place appendices at the end of chapters rather

than at the end of the thesis. This can make your chapters more self-contained.

4

Chapter 2

Files

Thesis in a Box consists of a set of files, some of which you will change, and others

which you will not. You will change the following files:

• frontmatter.sty, which customizes the information in the front matter (e.g.,

thesis title, your name, etc.)

• abstract.tex, the LATEX source of your abstract

• acknowledgements.tex, the LATEX source of your acknowledgements

• commands.tex, the LATEX source of all the extra commands you want included

in the document, like package includes and command definitions

• content.tex, the LATEX source of your thesis

• thesis.bib, the BibTEX file containing your bibliography information

Do not change the following files, unless you know what you’re doing:

• thesis.tex, the LATEX file that collects together several LATEX files to form your

complete thesis

5

Chapter 2. Files

• frontmatter.tex, the LATEX source of the front matter, including the title page,

table of contents, etc.

• hyperref.cfg, which customizes the PDF translation

• named.sty and named.bst, which implement the “named” BibTEX style

• Makefile, which allows you to compile your thesis easily using make

6

Chapter 3

Compiling your thesis

The Makefile distributed with Thesis in a Box has been designed to perform the

following functions if and when they are needed:

• Compiling the sources using pdflatex

• Creating the bibliography using bibtex

• Creating the index using makeindex

It is also sensitive to when LATEX must be run multiple times to resolve cross-

references. There are two commands that are useful:

1. make: this performs all of the tasks above, resulting in the PDF file

2. make clean: this removes the PDF file as well as any intermediate files made

by the make process. It does not remove other files like E-macs ~ files.

To view your thesis, you can use Acrobat Reader or another PDF viewer such

as Apple Preview. While you are writing your thesis, I recommend using xpdf as

a viewer, because you can quickly reload the PDF file to reflect editing changes by

simply typing r.

7

Chapter 4

Conclusion

4.1 Contributions of this thesis

Okay, so Thesis in a Box is not as impressive as Einstein’s famous relation between

matter and energy:

E = mc2 (4.1)

But I hope it saves you some time.

4.2 Directions for future research

If anyone sees a nice way to improve Thesis in a Box, please let me know (or better

yet, do it and send me the result).

8

Bibliography

[Murphy, 2002] Kevin Murphy. Dynamic Bayesian Networks: Representation, Infer-ence and Learning. PhD thesis, University of California, Berkeley, 387 Soda Hall,Berkeley CA 94720, July 2002.

[Paskin, 2003] Mark A. Paskin. Thesis in a Box. University of California, Berkeley,387 Soda Hall, Berkeley CA 94720, August 2003.

9

Index

item, 2

10