Jackson Laboratory Paper Template

Created by: Kumar Lab, The Jackson Laboratory GitHub: https://github.com/vivekJax/KumarLab-LatexTemplate-light

License: Proprietary — Jackson Laboratory use only (see LICENSE)

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Sample Output

EB Garamond (Traditional — default)	Source Sans Pro (Modern)

Full PDFs: sample_garamond.pdf · sample_sourcesans.pdf

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Choose Your Template

jax_main.tex — Full Paper (Modular)

• Best for: Multi-section research papers, collaborative writing
• Structure: Each section in its own file (01_introduction.tex, 02_methods.tex, etc.)
• Why: Multiple authors can work on different sections simultaneously

jax_simple.tex — Quick Document (Single File)

• Best for: Short reports, memos, single-author documents
• Structure: Everything in one file — no external section files needed
• Why: Fast to start, nothing to set up, just write

Both templates use jacksonlab.sty for formatting, so they look identical in the final PDF.

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Quick Start

1. Pick your template

• Full paper? Open jax_main.tex and edit the section files
• Quick document? Open jax_simple.tex and write directly

2. Choose your font

\usepackage[garamond]{jacksonlab}   % Traditional serif (EB Garamond) — default
\usepackage[sourcesans]{jacksonlab} % Modern humanist sans-serif

3. Compile

# Quick compilation
./scripts/compile_simple.sh

# With bibliography
./scripts/compile_with_bibtex.sh

# Or manually
xelatex jax_main.tex

4. View your PDF

Open jax_main.pdf (or jax_simple.pdf) to see your paper.

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Font Options

Font	Option	Style	Best For
EB Garamond	garamond	Classic humanist serif	Traditional academic publications — default
Source Sans Pro	sourcesans	Modern humanist sans-serif	Contemporary research papers

All headers and titles use TeX Gyre Heros (Helvetica clone). All fonts ship with TeX Live — no system fonts or bundled files needed. Works on Windows, Linux, and macOS.

EB Garamond (Traditional)	Source Sans Pro (Modern)

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What to Edit

Title Page (in your chosen template)

% Title
\titletext{Your Title First Line}{Second Line}

% Authors (* = Equal contribution, † = Correspondence, ‡ = Senior author)
{\authorfont First Author*, Second Author†, Third Author‡}

% Institution
{\affiliationfont The Jackson Laboratory \\ 600 Main Street, Bar Harbor, ME 04609, USA}

% Abstract
{\abstractfont Your abstract text here.}

Content

Full paper (jax_main.tex): Edit the section files:

• 01_introduction.tex — Introduction
• 02_methods.tex — Methods
• 03_results.tex — Results
• 04_discussion.tex — Discussion
• 05_supplement.tex — Supplementary materials

Quick document (jax_simple.tex): Write sections directly in the file.

References

Add entries to references.bib, then cite with \cite{key} in your text.

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File Structure

Your Project/
├── jax_main.tex              # Full paper template (modular)
├── jax_simple.tex            # Quick document template (single file)
├── jacksonlab.sty            # Style package (shared by both templates)
├── 01_introduction.tex       # Introduction (used by jax_main.tex)
├── 02_methods.tex            # Methods (used by jax_main.tex)
├── 03_results.tex            # Results (used by jax_main.tex)
├── 04_discussion.tex         # Discussion (used by jax_main.tex)
├── 05_supplement.tex         # Supplement (used by jax_main.tex)
├── references.bib            # Bibliography
├── figures/                  # Figures folder
│   └── JAX logo.png
└── scripts/                  # Compilation scripts
    ├── compile_simple.sh
    ├── compile_with_bibtex.sh
    └── watch_latex.sh

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Compilation

Method	Command	When to Use
Simple	./scripts/compile_simple.sh	Editing text, quick preview
Full	./scripts/compile_with_bibtex.sh	Added/changed references
Watch	./scripts/watch_latex.sh	Active writing, auto-recompile on save
Manual	xelatex jax_main.tex	Direct compilation

Requirement: Must use XeLaTeX (not pdfLaTeX) for font support.

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Adding Content

Figures

\begin{figure}[h]
\centering
\includegraphics[width=0.8\textwidth]{figures/your_figure.png}
\caption{Your figure caption.}
\label{fig:your_figure}
\end{figure}

Tables

\begin{table}[h]
\centering
\begin{tabular}{lcc}
\toprule
Method & Accuracy & Speed \\
\midrule
Method A & 95\% & Slow \\
Method B & 94\% & Fast \\
\bottomrule
\end{tabular}
\caption{Your table caption.}
\label{tab:your_table}
\end{table}

Citations

Add to references.bib:

@article{key,
  title={Title},
  author={Author},
  journal={Journal},
  year={2024}
}

Then cite: \cite{key}

Run ./scripts/compile_with_bibtex.sh after adding new references.

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Troubleshooting

Problem	Solution
Fonts look wrong	Make sure you're using xelatex, not pdflatex
References show [?]	Run ./scripts/compile_with_bibtex.sh
xelatex: command not found	Add TeX Live to your PATH (e.g. export PATH=/usr/local/texlive/2025/bin/x86_64-linux:$PATH)
Permission denied on scripts	Run chmod +x scripts/*.sh
Style not loading	Make sure jacksonlab.sty is in the same folder as your .tex file

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Customization

Font Sizes

Edit jacksonlab.sty:

\newcommand{\titlefont}{\fontsize{20}{28}\selectfont\bfseries\sffamily}
% Change 20 to 18 (smaller) or 22 (larger)

Title Box Colors

Edit jacksonlab.sty:

\newtcolorbox{titlebox}{
    colback=gray!10,  % Change to white, blue!10, etc.

Tables

The template provides table helpers: gray alternating rows, left-aligned cells with hanging indent.

\begin{table}[h!]
\centering
\begin{minipage}{\mytablewidth}
\centering
\sffamily\small
{\setlength{\tabcolsep}{0pt}%
\begin{tabular}{@{}L{3cm}L{2.5cm}L{\dimexpr\mytablewidth-3cm-2.5cm\relax}@{}}
\toprule
\textbf{Col 1} & \textbf{Col 2} & \textbf{Col 3} \\
\midrule
\gr Shaded row & data & data \\
Unshaded row & data & data \\
\bottomrule
\end{tabular}}
\end{minipage}
\caption{Your caption.}
\end{table}

• L{width} — left-aligned column with hanging indent on wrap
• \gr — gray shading for alternating rows
• \mytablewidth — consistent width matching page margins

Captions

When using the garamond option, captions render in EB Garamond at 9pt. No configuration needed.

Long URLs

If a paragraph with a long URL overflows, wrap it:

\begin{sloppypar}
Your paragraph with a long \url{https://example.com/very/long/path} here.
\end{sloppypar}

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VS Code / Cursor Setup

Recommended Extensions

1. LaTeX Workshop — LaTeX support, auto-compilation, PDF preview
2. BibTeX Language Support — Syntax highlighting for .bib files

LaTeX Workshop Settings

Add to your settings.json to use XeLaTeX:

"latex-workshop.latex.tools": [
  {
    "name": "xelatex",
    "command": "xelatex",
    "args": ["-interaction=nonstopmode", "-synctex=1", "%DOC%"]
  }
],
"latex-workshop.latex.recipes": [
  {
    "name": "xelatex + bibtex",
    "tools": ["xelatex", "bibtex", "xelatex", "xelatex"]
  }
]