manuscript-formatting

Name: manuscript-formatting
Author: neuromechanist

37stars7forks

How to install manuscript-formatting?

neuromechanist/research-skills/manuscript-formatting

$npx -y skills add neuromechanist/research-skills --skill manuscript-formatting

Installs into the current project.

Summary

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 want

Files · 1

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SKILL.md

1	# Manuscript Formatting and Submission Preparation
2
3	Format manuscripts to meet journal-specific requirements and prepare submission packages.
4
5	## When to Use
6
7	- Formatting a manuscript for a specific journal
8	- Preparing a submission package (cover letter, figures, supplementary)
9	- Converting between formats (Word to LaTeX, markdown to LaTeX)
10	- Checking compliance with author guidelines
11	- Managing references and BibTeX
12
13	## Common Journal Formats
14
15	### IEEE
16	- Template: IEEEtran class
17	- Columns: Two-column
18	- References: Numbered, [1] style
19	- Figures: Fit within column or span both columns
20	- Page limit: Varies (typically 6-8 for conference, 12-14 for journal)
21
22	```latex
23	\documentclass[journal]{IEEEtran}
24	\usepackage{cite}
25	\usepackage{amsmath}
26	\usepackage{graphicx}
27	```
28
29	### Nature/Science
30	- Format: Single column, specific heading hierarchy
31	- References: Superscript numbered
32	- Word limit: ~3000-5000 words (main text)
33	- Figures: Max 6-8, submitted as separate files
34	- Methods: Often separate section with no word limit
35
36	### PNAS
37	- Template: pnas-new class
38	- Columns: Two-column in print, single for review
39	- Word limit: ~4500 words
40	- References: Numbered
41	- Significance statement: Required, 120 words max
42
43	### PLoS ONE
44	- Format: No specific template required
45	- References: Numbered, Vancouver style
46	- No length restriction
47	- Data availability: Statement required
48
49	### Elsevier
50	- Template: elsarticle class
51	- Multiple formats: preprint, review, final
52	```latex
53	\documentclass[preprint,12pt]{elsarticle}
54	```
55
56	## LaTeX Essentials
57
58	### Document Structure
59	```latex
60	\documentclass[options]{class}
61	\usepackage{packages}
62
63	\title{Title}
64	\author{Authors}
65
66	\begin{document}
67	\maketitle
68	\begin{abstract}
69	\end{abstract}
70
71	\section{Introduction}
72	\section{Methods}
73	\section{Results}
74	\section{Discussion}
75
76	\bibliography{references}
77	\end{document}
78	```
79
80	### BibTeX Management
81
82	```bibtex
83	@article{smith2024,
84	author = {Smith, John and Doe, Jane},
85	title = {Title of the Paper},
86	journal = {Journal Name},
87	year = {2024},
88	volume = {10},
89	pages = {1--15},
90	doi = {10.1000/example}
91	}
92	```
93
94	Common BibTeX styles:
95	- `plain` - numbered, sorted alphabetically
96	- `unsrt` - numbered, order of citation
97	- `ieeetr` - IEEE transactions style
98	- `apalike` - APA-like author-year
99
100	### Cross-references
101	```latex
102	\label{fig:results} % Label a figure
103	\ref{fig:results} % Reference by number
104	Figure~\ref{fig:results} % Standard format
105	```
106
107	## Submission Checklist
108
109	### Before Submission
110	- [ ] Manuscript formatted per journal template
111	- [ ] Title page: title, authors, affiliations, corresponding author, ORCID
112	- [ ] Abstract within word limit
113	- [ ] Keywords provided (if required)
114	- [ ] Main text within page/word limit
115	- [ ] Figures as separate high-resolution files (typically 300+ DPI)
116	- [ ] Figure captions in a separate list
117	- [ ] Tables formatted per journal style
118	- [ ] References complete and consistently formatted
119	- [ ] Supplementary materials prepared separately
120	- [ ] Cover letter drafted (run `manuscript:humanizer` on it; cover letters are particularly prone to AI-tell phrasing)
121	- [ ] `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
122	- [ ] Conflict of interest statement
123	- [ ] Data availability statement
124	- [ ] Ethics approval statement (if applicable)
125	- [ ] Author contributions (CRediT format if required)
126	- [ ] Suggested reviewers (if required)
127
128	### Cover Letter Template
129
130	```
131	Dear Editor,
132
133	We submit our manuscript titled "{TITLE}" for consideration
134	in {JOURNAL}.
135
136	{1-2 sentences: what the study did and found}
137
138	{1-2 sentences: why this matters to the journal's readership}
139
140	{1 sentence: confirmation of originality and no concurrent submission}
141
142	We suggest the following reviewers:
143	1. {Name, Affiliation, Email}
144	2. {Name, Affiliation, Email}
145
146	Sincerely,
147	{Corresponding Author}
148	```
149
150	## Format Conversion
151
152	### Markdown to LaTeX
153	```bash
154	pandoc manuscript.md -o manuscript.tex --template=journal-template.tex --bibliography=refs.bib --citeproc
155	```
156
157	### Word to LaTeX
158	```bash
159	pandoc manuscript.docx -o manuscript.tex --extract-media=figures/
160	```
161
162	### LaTeX to Word (for journals requiring .docx)
163	```bash
164	pandoc manuscript.tex -o manuscript.docx --bibliography=refs.bib --citeproc
165	```
166
167	## Additional Resources
168
169	- Reference: [references/journal-requirements.md](references/journal-requirements.md) - Detailed requirements for major journals
170	- Reference: [references/latex-tr

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manuscript-formatting

37stars7forks

View on GitHub

How to install manuscript-formatting?

neuromechanist/research-skills/manuscript-formatting

$npx -y skills add neuromechanist/research-skills --skill manuscript-formatting

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Manuscript Formatting and Submission Preparation
2
3	Format manuscripts to meet journal-specific requirements and prepare submission packages.
4
5	## When to Use
6
7	- Formatting a manuscript for a specific journal
8	- Preparing a submission package (cover letter, figures, supplementary)
9	- Converting between formats (Word to LaTeX, markdown to LaTeX)
10	- Checking compliance with author guidelines
11	- Managing references and BibTeX
12
13	## Common Journal Formats
14
15	### IEEE
16	- Template: IEEEtran class
17	- Columns: Two-column
18	- References: Numbered, [1] style
19	- Figures: Fit within column or span both columns
20	- Page limit: Varies (typically 6-8 for conference, 12-14 for journal)
21
22	```latex
23	\documentclass[journal]{IEEEtran}
24	\usepackage{cite}
25	\usepackage{amsmath}
26	\usepackage{graphicx}
27	```
28
29	### Nature/Science
30	- Format: Single column, specific heading hierarchy
31	- References: Superscript numbered
32	- Word limit: ~3000-5000 words (main text)
33	- Figures: Max 6-8, submitted as separate files
34	- Methods: Often separate section with no word limit
35
36	### PNAS
37	- Template: pnas-new class
38	- Columns: Two-column in print, single for review
39	- Word limit: ~4500 words
40	- References: Numbered
41	- Significance statement: Required, 120 words max
42
43	### PLoS ONE
44	- Format: No specific template required
45	- References: Numbered, Vancouver style
46	- No length restriction
47	- Data availability: Statement required
48
49	### Elsevier
50	- Template: elsarticle class
51	- Multiple formats: preprint, review, final
52	```latex
53	\documentclass[preprint,12pt]{elsarticle}
54	```
55
56	## LaTeX Essentials
57
58	### Document Structure
59	```latex
60	\documentclass[options]{class}
61	\usepackage{packages}
62
63	\title{Title}
64	\author{Authors}
65
66	\begin{document}
67	\maketitle
68	\begin{abstract}
69	\end{abstract}
70
71	\section{Introduction}
72	\section{Methods}
73	\section{Results}
74	\section{Discussion}
75
76	\bibliography{references}
77	\end{document}
78	```
79
80	### BibTeX Management
81
82	```bibtex
83	@article{smith2024,
84	author = {Smith, John and Doe, Jane},
85	title = {Title of the Paper},
86	journal = {Journal Name},
87	year = {2024},
88	volume = {10},
89	pages = {1--15},
90	doi = {10.1000/example}
91	}
92	```
93
94	Common BibTeX styles:
95	- `plain` - numbered, sorted alphabetically
96	- `unsrt` - numbered, order of citation
97	- `ieeetr` - IEEE transactions style
98	- `apalike` - APA-like author-year
99
100	### Cross-references
101	```latex
102	\label{fig:results} % Label a figure
103	\ref{fig:results} % Reference by number
104	Figure~\ref{fig:results} % Standard format
105	```
106
107	## Submission Checklist
108
109	### Before Submission
110	- [ ] Manuscript formatted per journal template
111	- [ ] Title page: title, authors, affiliations, corresponding author, ORCID
112	- [ ] Abstract within word limit
113	- [ ] Keywords provided (if required)
114	- [ ] Main text within page/word limit
115	- [ ] Figures as separate high-resolution files (typically 300+ DPI)
116	- [ ] Figure captions in a separate list
117	- [ ] Tables formatted per journal style
118	- [ ] References complete and consistently formatted
119	- [ ] Supplementary materials prepared separately
120	- [ ] Cover letter drafted (run `manuscript:humanizer` on it; cover letters are particularly prone to AI-tell phrasing)
121	- [ ] `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
122	- [ ] Conflict of interest statement
123	- [ ] Data availability statement
124	- [ ] Ethics approval statement (if applicable)
125	- [ ] Author contributions (CRediT format if required)
126	- [ ] Suggested reviewers (if required)
127
128	### Cover Letter Template
129
130	```
131	Dear Editor,
132
133	We submit our manuscript titled "{TITLE}" for consideration
134	in {JOURNAL}.
135
136	{1-2 sentences: what the study did and found}
137
138	{1-2 sentences: why this matters to the journal's readership}
139
140	{1 sentence: confirmation of originality and no concurrent submission}
141
142	We suggest the following reviewers:
143	1. {Name, Affiliation, Email}
144	2. {Name, Affiliation, Email}
145
146	Sincerely,
147	{Corresponding Author}
148	```
149
150	## Format Conversion
151
152	### Markdown to LaTeX
153	```bash
154	pandoc manuscript.md -o manuscript.tex --template=journal-template.tex --bibliography=refs.bib --citeproc
155	```
156
157	### Word to LaTeX
158	```bash
159	pandoc manuscript.docx -o manuscript.tex --extract-media=figures/
160	```
161
162	### LaTeX to Word (for journals requiring .docx)
163	```bash
164	pandoc manuscript.tex -o manuscript.docx --bibliography=refs.bib --citeproc
165	```
166
167	## Additional Resources
168
169	- Reference: [references/journal-requirements.md](references/journal-requirements.md) - Detailed requirements for major journals
170	- Reference: [references/latex-tr

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Type