paper

name	paper
description	Scientific document builder — create papers, posters, slides, theses, reports from templates. Draft sections, peer review manuscripts, manage citations, compile LaTeX.
argument-hint	new <type> [title] | draft <section> [file] | review <file> | cite <doi|query> | compile [file] | templates
allowed-tools	Read Write Edit Bash Grep Glob WebSearch WebFetch
metadata	{"derived-from":"K-Dense-AI/claude-scientific-skills (MIT License)","original-skills":"scientific-writing, venue-templates, latex-posters, scientific-slides, peer-review, research-grants","templates-from":"delibae/claude-prism (apps/desktop/public/examples)"}

Paper — Scientific Document Builder

Create, draft, review, and compile scientific documents. Templates in artifacts/claude-prism-examples/.

Derived from K-Dense-AI/claude-scientific-skills (MIT) and claude-prism templates. Consolidated into a single Claude Code skill.

Usage

/paper new <type> [title]       # Scaffold a new document from template
/paper draft <section> [file]   # Write or expand a section (IMRAD-aware)
/paper review <file>            # Structured peer review of a manuscript
/paper cite <doi|arxiv|query>   # Look up and format citations as BibTeX
/paper compile [file]           # Compile LaTeX to PDF
/paper templates                # List available templates

Parse Arguments

Extract the subcommand (first token) and remaining arguments. If no arguments, show the usage block above and stop.

---

Available Templates

Type	Template Source	Document Class	Use For
paper	paper-standard/	article	Generic research paper
paper-ieee	paper-ieee/	IEEEtran	IEEE conference/journal
paper-acm	paper-acm/	ACM format	ACM conference/journal
poster	poster-academic/	article (A0)	Academic conference poster
slides	presentation-beamer/	beamer	Conference talk, seminar, defense
thesis	thesis-standard/	report	PhD/Master's thesis
report	report-scientific/	report	Lab/scientific report
report-tech	report-technical/	report	Technical report
letter	letter-formal/	letter class	Formal/cover letter
cv	cv-modern/	custom	Academic CV
book	book-standard/	book	Book/monograph
newsletter	newsletter/	custom	Newsletter
blank	blank/	article	Empty starting point

---

Subcommand Implementations

new <type> [title]

Create a new LaTeX document from a template.

Steps:

1. Match <type> against the template table above. If no match, show the table and stop.
2. Read the template .tex file from artifacts/claude-prism-examples/<template-dir>/main.tex.
3. If a references.bib exists in the template dir, read that too.
4. Ask the user for a target directory (default: current directory) and filename.
5. Customize the template:
   • Replace the placeholder title with the provided [title], or leave {Title} if none given.
   • Replace placeholder author/institution with {Author Name} / {Institution}.
   • Keep all structural sections intact.
   • For poster: preserve the color theme, font sizes, and multicol layout.
   • For slides: preserve the beamer theme and frame structure.
   • For thesis: preserve the declaration, abstract, acknowledgements, chapter structure.
6. Write the customized .tex file and .bib file (if applicable) to the target directory.
7. Report what was created and suggest next steps (e.g., /paper draft introduction my_paper.tex).

Type-specific guidance to include as LaTeX comments:

• paper / paper-ieee / paper-acm: IMRAD structure. Abstract 150-300 words. Introduction states contribution clearly.
• poster: A0 portrait. Max 800 words total. 5-6 sections. Title 72-120pt, headers 40-48pt, body 28-36pt. Three columns.
• slides: ~1 slide per minute. 60-70% visual, 30-40% text. Body font 24-28pt, titles 36-44pt.
• thesis: Front matter (declaration, abstract, acknowledgements, TOC). Main chapters. Appendices. Bibliography.
• report: Highlight boxes for key findings. Summary statistics tables. Note boxes for methodology details.

draft <section> [file]

Write or expand a section of an existing document.

Steps:

1. If [file] is provided, read it. Otherwise, search for .tex files in the current directory and ask which one.

2. Identify the document type from the \documentclass.

3. Locate the target <section> in the document. Section names are flexible — match against:

   • abstract, introduction, intro
   • methods, methodology, materials, approach, proposed, framework
   • results, experiments, evaluation
   • discussion, analysis
   • conclusion, summary, future
   • related, background, literature, prior
   • For slides: frame titles. For thesis: chapter names.

4. Apply the two-stage writing process:

   Stage 1 — Outline: Generate a structured outline of key points for the section:

   • 3-7 key points, each with 1-2 supporting sub-points
   • Identify citations needed (mark as \cite{needed:topic})
   • Identify figures/tables needed (mark as % TODO: Figure — description)
   • Present outline to user for approval

   Stage 2 — Prose: Convert approved outline to flowing scientific prose:

   • Write in full paragraphs (NEVER bullet points in the paper body)
   • Follow IMRAD conventions for the section type
   • Use precise, field-appropriate terminology
   • Maintain logical flow with transition sentences
   • Include equation environments where needed
   • Mark citation placeholders

5. Edit the section content into the .tex file using the Edit tool.

Section-specific writing guidance:

Section	Key Requirements
Abstract	Self-contained. State: problem, method, key result, implication. 150-300 words.
Introduction	Context → gap → contribution → outline. Final paragraph states contributions as numbered list.
Methods	Reproducible detail. Define all variables. State assumptions. Reference prior methods.
Results	Present findings without interpretation. One key message per figure/table. Statistical significance.
Discussion	Interpret results. Compare to prior work. Acknowledge limitations. State implications.
Conclusion	1-2 paragraphs. Summarize contribution (not results). Future directions.

review <file>

Structured peer review of a manuscript.

Steps:

1. Read the .tex or .pdf file.

2. Perform a systematic 7-stage review:

   Stage 1 — First Impression (30 seconds):

   • Novelty and significance assessment
   • Scope and fit for target venue
   • Overall quality impression

   Stage 2 — Section-by-Section:

   • Title/Abstract: Accuracy, completeness, word count
   • Introduction: Context, gap, contribution clarity
   • Methods: Reproducibility, rigor, completeness
   • Results: Presentation quality, statistical validity
   • Discussion: Interpretation accuracy, limitations acknowledged
   • References: Coverage, recency, self-citation balance

   Stage 3 — Technical Rigor:

   • Mathematical correctness (verify key derivations)
   • Statistical methods appropriate for data type
   • Experimental design (controls, replication, blinding)
   • Computational reproducibility (code, data availability)

   Stage 4 — Figures and Tables:

   • Quality, readability, colorblind accessibility
   • Axis labels, units, error bars, captions
   • Data integrity (consistent numbers across text/figures/tables)

   Stage 5 — Writing Quality:

   • Clarity, conciseness, grammar
   • Logical flow between sections and paragraphs
   • Jargon appropriate for audience

3. Output a structured review report:

## Summary Statement
[2-3 sentences on the paper's contribution and overall assessment]

## Major Issues (must address before publication)
1. [Issue with specific location and suggestion]
...

## Minor Issues (should address)
1. [Issue with line/section reference]
...

## Line-by-Line Comments
- L42: [specific comment]
...

## Questions for Authors
1. [Clarification needed]
...

## Recommendation
[ ] Accept as-is
[ ] Minor revision
[ ] Major revision
[ ] Reject

cite <identifier>

Look up a citation and format as BibTeX.

Steps:

1. Determine identifier type:

   • DOI (contains 10.): fetch metadata from https://doi.org/<doi> with Accept: application/x-bibtex
   • arXiv ID (e.g., 2103.14030): fetch from https://arxiv.org/abs/<id> and construct BibTeX
   • PMID (numeric): construct PubMed lookup URL
   • Free text query: use WebSearch to find the paper, extract DOI, then fetch BibTeX

2. For DOI resolution, use WebFetch:

   WebFetch("https://doi.org/<doi>", headers: {"Accept": "application/x-bibtex"})
   

3. Clean and format the BibTeX entry:

   • Generate a meaningful citation key: FirstAuthor2024keyword
   • Protect capitalization in titles with {}
   • Use -- for page ranges
   • Include DOI field
   • Remove unnecessary fields (abstract, month, keywords unless useful)

4. Output the formatted BibTeX entry.

5. If a .bib file exists in the current directory, offer to append the entry.

Batch mode: If multiple identifiers are provided (comma-separated or one per line), process each and combine.

compile [file]

Compile a LaTeX document to PDF.

Steps:

1. If [file] not given, find .tex files in current directory. Use the one that contains \begin{document}.
2. Check for LaTeX compiler availability:

   which pdflatex || which xelatex || which lualatex
   

3. If no compiler found, suggest installation:
   • Windows: MiKTeX or TeX Live (winget install MiKTeX.MiKTeX)
   • Check if latexmk is available for automated multi-pass compilation
4. Compile with the appropriate engine:

   # Standard compilation (handles references, TOC, etc.)
   pdflatex -interaction=nonstopmode <file> && \
   bibtex <basename> 2>/dev/null; \
   pdflatex -interaction=nonstopmode <file> && \
   pdflatex -interaction=nonstopmode <file>
   

   Or if latexmk is available:

   latexmk -pdf -interaction=nonstopmode <file>
   

5. Parse the log file for errors and warnings:
   • Errors: Report with line numbers and context
   • Warnings: Report overfull/underfull boxes, undefined references, missing citations
   • Success: Report page count and output PDF path
6. If errors occur, attempt to diagnose and fix common issues:
   • Missing packages: suggest \usepackage{} additions
   • Undefined control sequences: identify the command and suggest fixes
   • Missing files: check paths

templates

List all available templates with descriptions.

Steps:

1. Read the template directories in artifacts/claude-prism-examples/.
2. For each directory, check for main.tex and references.bib.
3. Display a formatted table showing:
   • Template name (the /paper new type argument)
   • Document class
   • Includes bibliography template (yes/no)
   • Brief description

---

Poster-Specific Guidance

When creating or drafting poster content, enforce these constraints:

• Content limit: Max 300-800 words total body text
• Section limit: 5-6 sections for A0, 4-5 for A1
• Font sizes: Title 72-120pt, section headers 40-48pt, body 28-36pt, references 24pt
• Layout: 3 columns for A0 portrait (use multicol)
• Color: Use a cohesive theme. Ensure colorblind accessibility (avoid red-green only distinctions)
• Figures: Large, clear, self-explanatory. Minimum 300 DPI
• Readability test: Can someone read it from 1.5 meters away?

Slides-Specific Guidance

When creating or drafting slides:

• Density: ~1 slide per minute of talk time
• Content split: 60-70% visual (figures, diagrams, equations), 30-40% text
• Font: Body 24-28pt minimum, titles 36-44pt
• Structure: Title → Outline → Background → Methods → Results → Conclusion → Questions
• Anti-patterns: No walls of text. No full sentences (use key phrases). No more than 6 bullet points per slide.
• Talk types:
  • Conference (10-20 min): 10-15 content slides + title/questions
  • Seminar (45-60 min): 30-40 content slides
  • Defense (60 min): 35-45 slides + backup slides
  • Lightning (5 min): 5-7 slides, no outline slide

Grant-Specific Guidance

When creating grant proposals (use report or blank template):

• NSF: Intellectual Merit + Broader Impacts. 15-page project description. Specific Aims first.
• NIH: Significance, Innovation, Approach, Investigators, Environment. R01 = 12 pages.
• DOE: Technical narrative. Mission relevance. Milestones and deliverables.
• General: State objectives in first paragraph. Use preliminary data. Include timeline figure. Budget justification should be detailed but concise.

Error Handling

• If <type> doesn't match any template: show the template table
• If <section> not found in document: list the sections present and ask which one
• If <file> doesn't exist: report not found
• If no .tex files found: suggest /paper new <type>
• If LaTeX compiler not found: provide installation instructions
• If no arguments given: show usage block