# Manuscript Formatting

> Use this skill for \"format manuscript\", \"prepare for submission\", \"journal formatting\", \"LaTeX template\", \"submission checklist\", \"format references\", \"BibTeX\", \"author guidelines\", \"page limits\", \"format for Nature\", \"format for IEEE\", or when the user wants to format a manuscript for journal submission.

- **Type:** Skill
- **Install:** `agentstack add skill-neuromechanist-research-skills-manuscript-formatting`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [neuromechanist](https://agentstack.voostack.com/s/neuromechanist)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** BSD-3-Clause
- **Upstream author:** [neuromechanist](https://github.com/neuromechanist)
- **Source:** https://github.com/neuromechanist/research-skills/tree/main/plugins/manuscript/skills/manuscript-formatting

## Install

```sh
agentstack add skill-neuromechanist-research-skills-manuscript-formatting
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Manuscript Formatting and Submission Preparation

Format manuscripts to meet journal-specific requirements and prepare submission packages.

## When to Use

- Formatting a manuscript for a specific journal
- Preparing a submission package (cover letter, figures, supplementary)
- Converting between formats (Word to LaTeX, markdown to LaTeX)
- Checking compliance with author guidelines
- Managing references and BibTeX

## Common Journal Formats

### IEEE
- **Template:** IEEEtran class
- **Columns:** Two-column
- **References:** Numbered, [1] style
- **Figures:** Fit within column or span both columns
- **Page limit:** Varies (typically 6-8 for conference, 12-14 for journal)

```latex
\documentclass[journal]{IEEEtran}
\usepackage{cite}
\usepackage{amsmath}
\usepackage{graphicx}
```

### Nature/Science
- **Format:** Single column, specific heading hierarchy
- **References:** Superscript numbered
- **Word limit:** ~3000-5000 words (main text)
- **Figures:** Max 6-8, submitted as separate files
- **Methods:** Often separate section with no word limit

### PNAS
- **Template:** pnas-new class
- **Columns:** Two-column in print, single for review
- **Word limit:** ~4500 words
- **References:** Numbered
- **Significance statement:** Required, 120 words max

### PLoS ONE
- **Format:** No specific template required
- **References:** Numbered, Vancouver style
- **No length restriction**
- **Data availability:** Statement required

### Elsevier
- **Template:** elsarticle class
- **Multiple formats:** preprint, review, final
```latex
\documentclass[preprint,12pt]{elsarticle}
```

## LaTeX Essentials

### Document Structure
```latex
\documentclass[options]{class}
\usepackage{packages}

\title{Title}
\author{Authors}

\begin{document}
\maketitle
\begin{abstract}
\end{abstract}

\section{Introduction}
\section{Methods}
\section{Results}
\section{Discussion}

\bibliography{references}
\end{document}
```

### BibTeX Management

```bibtex
@article{smith2024,
  author  = {Smith, John and Doe, Jane},
  title   = {Title of the Paper},
  journal = {Journal Name},
  year    = {2024},
  volume  = {10},
  pages   = {1--15},
  doi     = {10.1000/example}
}
```

Common BibTeX styles:
- `plain` - numbered, sorted alphabetically
- `unsrt` - numbered, order of citation
- `ieeetr` - IEEE transactions style
- `apalike` - APA-like author-year

### Cross-references
```latex
\label{fig:results}   % Label a figure
\ref{fig:results}     % Reference by number
Figure~\ref{fig:results}  % Standard format
```

## Submission Checklist

### Before Submission
- [ ] Manuscript formatted per journal template
- [ ] Title page: title, authors, affiliations, corresponding author, ORCID
- [ ] Abstract within word limit
- [ ] Keywords provided (if required)
- [ ] Main text within page/word limit
- [ ] Figures as separate high-resolution files (typically 300+ DPI)
- [ ] Figure captions in a separate list
- [ ] Tables formatted per journal style
- [ ] References complete and consistently formatted
- [ ] Supplementary materials prepared separately
- [ ] Cover letter drafted (run `manuscript:humanizer` on it; cover letters are particularly prone to AI-tell phrasing)
- [ ] `manuscript:humanizer` natural-writing pass applied to all narrative sections, *then* journal house style (title case, citation format, etc.) re-applied where it overrides humanizer defaults
- [ ] Conflict of interest statement
- [ ] Data availability statement
- [ ] Ethics approval statement (if applicable)
- [ ] Author contributions (CRediT format if required)
- [ ] Suggested reviewers (if required)

### Cover Letter Template

```
Dear Editor,

We submit our manuscript titled "{TITLE}" for consideration
in {JOURNAL}.

{1-2 sentences: what the study did and found}

{1-2 sentences: why this matters to the journal's readership}

{1 sentence: confirmation of originality and no concurrent submission}

We suggest the following reviewers:
1. {Name, Affiliation, Email}
2. {Name, Affiliation, Email}

Sincerely,
{Corresponding Author}
```

## Format Conversion

### Markdown to LaTeX
```bash
pandoc manuscript.md -o manuscript.tex --template=journal-template.tex --bibliography=refs.bib --citeproc
```

### Word to LaTeX
```bash
pandoc manuscript.docx -o manuscript.tex --extract-media=figures/
```

### LaTeX to Word (for journals requiring .docx)
```bash
pandoc manuscript.tex -o manuscript.docx --bibliography=refs.bib --citeproc
```

## Additional Resources

- Reference: [references/journal-requirements.md](references/journal-requirements.md) - Detailed requirements for major journals
- Reference: [references/latex-troubleshooting.md](references/latex-troubleshooting.md) - Common LaTeX issues and fixes

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [neuromechanist](https://github.com/neuromechanist)
- **Source:** [neuromechanist/research-skills](https://github.com/neuromechanist/research-skills)
- **License:** BSD-3-Clause

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-neuromechanist-research-skills-manuscript-formatting
- Seller: https://agentstack.voostack.com/s/neuromechanist
- Browse the marketplace: https://agentstack.voostack.com/browse

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