How it works

When you need this page: Optional

Why LaTeX can suit a thesis, what happens when you press Compile, and how the files fit together. You don't need this page to write, but it helps you decide whether LaTeX suits you and, when something looks odd, find the next step.

On this page

Learn a few commands, then let the shared formatting handle the repetition. You type or paste your text, and one file of formatting rules (the class file, rpi-thesis.cls) keeps headings, numbering, and spacing consistent. You still check the PDF.

Why LaTeX for a thesis

Keep your attention on the chapter you are writing. Let shared rules handle the repetition.

One chapter at a timeSmall files. One connected thesis.

Let the numbers followMove chapters. Keep references linked.

Shared formattingOne class sets the shared rules.

Reuse your sourceAdapt text and figures for another format.

Leave stray styles behindKeep the words, without imported fonts.

Keep citations connectedCite by key. Let the reference list follow.

Word can automate too. Its styles and fields need to be kept in step (opens in a new tab), and pasted text can bring its own formatting (opens in a new tab). LaTeX was built for mathematics, so displayed equations are laid out and numbered for you. It is free, and your files are plain text that back up like any folder.

You only need about 10 commands. A command is a short instruction that starts with a backslash, such as \section{Methods}. Headings, citations, cross-references, figures, tables, and equations cover most of a thesis, and they fit in one table at the top of writing basics. For references, choose the citation style and matching commands.

Change one word, watch the layout

The same words can look very different under another set of formatting rules. This teaching example uses the American Mathematical Society's amsart class (opens in a new tab) for one column. Change amsart to IEEEtran (opens in a new tab) in \documentclass{amsart}, compile again, and the headings, captions, spacing, and columns follow the new class.

Change the class nameamsartIEEEtran

\documentclass{amsart}

First page of the shared teaching example in amsart: one column, centered headings. — Top of page 1 of 2. Same source; only the class name changes.

View larger

\documentclass{IEEEtran}

First page of the shared teaching example in IEEEtran: two columns, Roman-numbered headings. — Top of page 1 of 1. Same source; only the class name changes.

View larger

In words: one example, two academic layouts. Only the class name changes.

Note: this article example does not use the RPI thesis starter. A real chapter-to-paper move also means adapting thesis-only commands, then checking the PDF.

Optional: try the one-word change yourself

In a separate, empty LaTeX project on your computer or Overleaf, paste this example into the main file and compile. Replace amsart with IEEEtran on the first line and compile again. Leave your thesis project as it is. A missing .cls error means that class is not installed.

The pictures above are compiled from this example and show the first page of each version. The counts in the example are invented for teaching.

\documentclass{amsart}
\usepackage[T1]{fontenc}
\usepackage{amsmath}
\title{Grouping a Small Reading List}
\author{A teaching example}
\date{}
\begin{document}
\maketitle
\section{Start with a question}
A reading list can grow faster than the notes that explain it. A useful first
step is to give every note a purpose: background, method, or discussion.
These labels describe what a note contributes to the current question. They
do not rank the quality of a source or replace a careful reading of it.

This short document uses invented counts to demonstrate headings, a table,
an equation, a figure, and references to numbered items. It reports no
research findings. The same source can be compiled with two document classes
so that the effect of the formatting rules is visible.

Suppose a reader begins with a folder of notes collected during an early
literature search. Some notes define terms, others explain procedures, and
others record disagreements or open questions. The folder becomes easier to
navigate when those roles are explicit. A note may still link to more than
one topic; the group is only a starting point for finding it again.
\section{Describe the collection}
Table~\ref{tab:notes} gives a small example. The counts describe notes rather
than publications: one publication might produce several notes, and a
single note might connect ideas from several publications. Keeping that
unit clear avoids confusing the size of the collection with its coverage.

\begin{table}[htbp]
\caption{Invented counts for three groups of notes.}
\label{tab:notes}
\centering
\begin{tabular}{lr}
\hline
Group & Notes \\
\hline
Background & 12 \\
Methods & 18 \\
Discussion & 15 \\
\hline
\end{tabular}
\end{table}

The arithmetic mean provides one description of the group sizes:
\begin{equation}
\bar{x}=\frac{1}{n}\sum_{i=1}^{n}x_i.
\label{eq:mean}
\end{equation}
For the three counts in Table~\ref{tab:notes}, Equation~\ref{eq:mean} gives a
mean of fifteen notes per group. That number says nothing about whether the
reading list is complete. A small group might contain the most useful
source, while a large group might repeat the same point many times.
\section{Review the organization}
The sequence in Figure~\ref{fig:review} is a reminder to revisit the groups.
Read a source, record its contribution, then review where the note belongs.
A label chosen early in a project may become less useful when the question
changes. Moving a note is part of organizing the collection, rather than a
sign that the first arrangement was wrong.

\begin{figure}[htbp]
\centering
\setlength{\unitlength}{1pt}
\begin{picture}(210,34)
\put(0,7){\framebox(54,22){Read}}
\put(54,18){\vector(1,0){24}}
\put(78,7){\framebox(54,22){Group}}
\put(132,18){\vector(1,0){24}}
\put(156,7){\framebox(54,22){Review}}
\end{picture}
\caption{A short sequence for revisiting a reading list.}
\label{fig:review}
\end{figure}

A useful review asks whether each group still answers a distinct question.
If two groups always contain the same notes, they may be easier to use as
one group. If a group contains several unrelated topics, a more specific
label may help. The purpose is to make the next writing session easier,
without spending more time organizing than reading and thinking.
\section{Keep enough context}
A brief note should say why the source mattered when it was read. A copied
sentence without context can be hard to interpret later. Recording the
question, the relevant page, and the source's role gives the reader a route
back to the original material. The original source remains the place to
check an interpretation before using it in a draft.

It can also help to distinguish a summary from a question or a proposed
connection. Those are different kinds of notes, even when they sit beside
each other. A clear label preserves that distinction when the collection is
revisited after a long break. No particular note-taking application is
needed for this exercise.
\section{Read the page as well as the source}
The document class decides how the title, headings, captions, and columns
appear. The source identifies their roles rather than fixing each item at
a position on a page. Paragraphs wrap to the available width, and figures
or tables may move to make room for surrounding text.

In both versions, the equation, table, figure, and cross-references contain
the same information. The single-column and two-column pages arrange that
information differently. Look at the heading styles and caption numbering
as well as the column widths: several formatting choices follow from the
same class-name change.

This example uses commands shared by both classes. A real journal paper
also needs the venue's author instructions, suitable references, and a
check of every page. Reusing content can save repeated formatting work;
it does not remove the need to revise the argument for its audience.
\end{document}

The honest costs

A first week of getting used to it. You see the formatted page when you compile, not as you type.
Errors look scary. They are long, but the useful part names a file and a line (read an error message).
Advisors who prefer Word. Send a PDF to comment on, or a Word copy, and apply their edits by hand (common situations).
Tables take a bit more effort. Paste spreadsheet cells into Convert to LaTeX, or adapt the sample chapters' example.
The Office of Graduate Education (OGE) can't debug LaTeX. Its staff review your formatting, not your code (ask for help).

When Word might still make sense

Your thesis is short, with no equations and few figures or tables.
Your committee edits only in Word, and you would rather not manage review copies.
You must submit within days and have never used LaTeX.

OGE provides its own Word template, available from the OGE submission page (opens in a new tab). Either route can lead to a thesis OGE accepts.

An AI chat can help you get unstuck, as one route beside web search and community help (AI for technical help).

Your words and your formatting are separate

Each chapter is its own file, your sources live in references.bib, and your images live in figures/. One more file, rpi-thesis.cls, is the formatting engine: margins, spacing, page numbers, headings, captions, and the title page. Your files hold content and settings, and never say how a page should look.

Swapping the class file. On the left, your files (metadata.tex, frontmatter, chapters, appendices, figures, references.bib, preamble.tex) stay exactly as they are. In the middle, an old rpi-thesis.cls is replaced with a new one, with a note that this is for compatible updates and to see the changelog. On the right, recompiling produces a PDF with the same words in the updated formatting.

In words: your files + rpi-thesis.cls give your PDF. Replace the class file, recompile, and the same words come out with the updated formatting (check the changelog first: an update may need other edits, see update the formatting safely).

So when OGE changes a rule or the toolkit fixes something, you usually replace one file and your chapters are untouched.

That is also why you normally leave the class file alone: edits there would be lost in the next update. (If you know Word, formatting lives with your text there; here it lives in one separate file.)

What the class takes care of on every page:

Two thesis pages. Front matter (ABSTRACT): heading at the top margin, centered, bold; double-spaced text; 1 inch margins on all sides; roman page number (vi) bottom center, 0.75 inch from the edge. Body page: arabic page number top right, 0.75 inch from the edge; bold table caption above the table and bold figure caption below the figure; single-spaced footnotes. Chapter-opening pages put the number at the bottom center. Margins, page numbers, spacing, and caption style are set once in rpi-thesis.cls.

In words: 1-inch margins, page numbers in the right place (roman, then arabic), double spacing, bold captions, and single-spaced footnotes. You still type your headings and decide where each caption goes.

What each file does

Which file changes which part of the PDF. On the left, five project files; on the right, pages of main.pdf. metadata.tex points to the title page, with your title, name, and degree. main.tex points to the contents: it sets the order of the chapters. chapters/ points to a chapter page: these files hold your words. references.bib and preamble.tex point to the reference list: they set the citation style and the references. rpi-thesis.cls points to a dashed frame around the whole PDF: it sets the formatting of every page and is normally never edited.

In words: metadata.tex fills the title page, main.tex sets the order, chapters/ hold your words, references.bib and preamble.tex make the citations and reference list, and rpi-thesis.cls formats every page.

File or folder	What it is	Do you edit it?
`main.tex`	The file you compile; lists the pieces in order	To add or remove chapters
`metadata.tex`	Your title, name, degree, and committee	Yes, first
`frontmatter/`	Abstract and acknowledgments	Yes
`chapters/`	One file per chapter	Yes: you write here
`appendices/`	Supplementary material	If you need it
`figures/`	Your images	Add files here
`references.bib`	Your sources, one entry each	Through Zotero, or by hand
`preamble.tex`	Extra packages (add-ons) and the citation style	Rarely
`rpi-thesis.cls`	The formatting rules	Normally never
`assets/`	Where the RPI seal you download goes	Once, to add the seal
`build/`	Output from the build helper or VS Code	No, it is regenerated

What "compiling" does

Compiling turns your plain-text .tex files into a PDF. A full compile runs several programs in a row, repeated as needed:

Build pipeline. Step 1: pdfLaTeX reads main.tex and writes notes about labels, headings, and the citations it needs. Step 2: Biber reads that citation list and references.bib and writes a formatted reference list. Step 3: pdfLaTeX runs again and places the references. Step 4: pdfLaTeX runs once more so page numbers in the contents and cross-references settle. One Compile runs these steps as often as needed. The result is main.pdf.

pdfLaTeX lays out the pages and writes notes to itself: which labels and headings exist, and which citations you used. At this point a citation shows its key in bold, like [lamport1994], cross-references show ??, and the contents page is empty.
The bibliography step (a program called Biber) reads those notes and references.bib, and writes the formatted reference list (.bbl). The PDF does not change yet.
pdfLaTeX reads the .bbl: the citation becomes [1], the ?? become chapter numbers, and the contents fill in.
pdfLaTeX once more settles page numbers in the contents and cross-references, which shifted when the references appeared.

Chapter 1 after step 1. The sentence reads "a real citation example [lamport1994]" with the key in bold, then "Chapter ?? contains small examples you can adapt, and Chapter ?? closes the document." — Chapter 1 after step 1

Chapter 1 after step 3: "a real citation example [1]", then "Chapter 2 contains small examples you can adapt, and Chapter 3 closes the document." — Chapter 1 after step 3

Overleaf and VS Code run every step for you each time you compile, repeating passes until the output stops changing (via a tool called latexmk). The extra files (.aux, .bbl, .toc, ...) are scratch notes you never edit; the .log file holds the full error messages and is worth reading.

Bold citation keys and question marks

A citation key in bold, ?? where a number should be, or an empty contents page is LaTeX saying "I haven't finished filling this in yet": the notes from one pass are read on the next. Compile again; if it stays, the fixes are in fixing problems.

Where the PDF ends up

How you compile	Your PDF
VS Code (with the starter's settings)	The tab beside your text; the file is `build/main.pdf`
Overleaf	The preview pane; use its download button for a copy
Another editor, TeXShop, TeXworks, or TeXstudio	Usually `main.pdf`, next to `main.tex`
Optional build commands in a terminal	`build/main.pdf` (build helper) or `main.pdf` (`latexmk`)

Switched methods? Open the PDF from the method you just used, not an old copy.

Your computer or Overleaf?

Your computer compared with Overleaf. Both start from the same project files and run the same compile steps (pdfLaTeX, Biber, then pdfLaTeX again as often as needed), so they produce matching PDFs when both use the same files, engine, packages, and fonts. On your computer the files live in a folder you control, LaTeX is installed locally, and you work offline in an editor. On Overleaf the files and the LaTeX installation live on Overleaf's servers and you work in a browser.

Same files, same programs; only where things live differs. The PDFs match when both use matching files, engine, packages, and fonts. Overleaf lets you choose the TeX distribution version in its settings. To move or use both, see going further.

The suggested workflow, and why

A thesis is not just a document you format at the end. This is one way to connect drafting, advisor feedback, sources, and figures. It is a suggestion, not a rule; you and your advisor decide how you work.

View larger

In words: draft and discuss, move stable sections into chapter files, then compile and review the thesis. After a section moves, revise its .tex file; changes do not flow back to the drafting app.

Required versus suggested. OGE's manual and your degree checklist, on the OGE submission page (opens in a new tab), are what count, and they win over anything here (submitting). rpi-thesis.cls is the toolkit's reading of those rules, starting from RPI's official LaTeX template on RPI ITS's Thesis Preparation page (opens in a new tab), so you still check the PDF (what OGE commonly flags). Everything else here, from drafting apps and Zotero to optional helpers, is a convenience you can swap out.

The short version (the steps overlap and repeat):

Talk about your research early. Feedback on your argument is worth more before the layout matters. Already have a stable draft or published papers? Bring them in now.
Draft where you and your advisor are comfortable (below). At ease in LaTeX? Drafting in the chapter files skips the move later.
Keep references and figure sources organized. Save real source records in a citation manager while you read, and keep each figure's data or editable drawing beside it in figures/. With only a few sources, pasting entries by hand is fine.
Move stable material in gradually, one section or chapter at a time. Try one small section early, with a figure and a few citations, so any conversion problems show up long before a deadline.
Compile and look through the whole PDF every so often, not only at the end. Before you submit, use the final PDF checklist.

More recipes are in going further.

Draft where you and your advisor can work comfortably

Use what lets you and your advisor read, comment, and revise without friction; you don't need a new app to start. If you are choosing, this guide suggests a Markdown tool: plain text with a few symbols for structure, such as # before a heading. You never need to learn it to use this toolkit, but your draft stays a readable file in any editor, and free tools such as Pandoc can convert it to LaTeX, Word, or slides. Four apps, for different situations:

Obsidian (opens in a new tab): Markdown files on your own computer. You can share a vault (a folder of notes), but that is not simultaneous editing of one file (Obsidian: collaborate on a shared vault (opens in a new tab)).
HackMD (opens in a new tab): collaborative Markdown in your browser.
Google Docs (opens in a new tab): live co-writing and comments, familiar to many advisors.
Notion (opens in a new tab): if you already use it. It is block-based, not a folder of Markdown files, but it can export your pages as Markdown (opens in a new tab).

App-specific links, embeds, citations, and math syntax may need cleanup when you export. Word works too, for an existing draft or an advisor who reviews in Word (from Word or Google Docs, an advisor wants Word).

Reuse your material elsewhere

One source, many destinations. Your content files (chapters, figures, and references.bib) sit in the middle. Arrows lead outward to: the thesis PDF, through rpi-thesis.cls; a journal or conference paper, through the venue's class such as IEEEtran or acmart; slides, through Beamer; a Word copy for reviewers, through Pandoc; and a web page. A caption reads "a world of possibilities, not a to-do list".

In words: your chapters and sources sit in the middle; the thesis PDF is the one destination you need, and the others are options.

Reuse is a head start, not a copy: each output needs its own template, some cleanup, and a check against its own requirements, and this toolkit's formatting is only for RPI graduate theses. Going further has recipes.

One habit pays off everywhere: a citation typed as text, such as "(Lamport, 1994)", is not a citation key such as lamport1994. Only the key, matched to an entry in references.bib, lets LaTeX build the citation and reference list, so collect real records early and keep their keys stable. For a tool for a specific task, try the helper picker or the How do I…? task index.

Want to learn more LaTeX?

Overleaf Learn (opens in a new tab) has friendly tutorials on almost every topic, whichever editor you use. CTAN (opens in a new tab) holds every package and its manual, including biblatex (opens in a new tab).

Something wrong or unclear on this page? Tell the maintainer (opens in a new tab), no account needed.