Nature-Style Scientific Figures
Yuan1z0825/nature-skills
Creates, revises, audits and exports manuscript-ready scientific figures in Python or R, and routes AI-generated graphical abstracts to a separate workflow.
A skill your agent uses when the user wants to write, structure, or revise academic paper sections, improve notation consistency, or refine figures and tables.
Install Paper Writing
$ npx skills add fcakyon/phd-skills --skill paper-writing -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install fcakyon/phd-skills paper-writing --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugin/skills/paper-writing .claude/skills/paper-writing && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "paper-writing" agent skill from https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writing into .claude/skills/paper-writing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-writing", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writingType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add fcakyon/phd-skills --skill paper-writing -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install fcakyon/phd-skills paper-writing --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/plugin/skills/paper-writing .agents/skills/paper-writing && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "paper-writing" agent skill from https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writing into .agents/skills/paper-writing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-writing", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add fcakyon/phd-skills --skill paper-writing -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install fcakyon/phd-skills paper-writing --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/plugin/skills/paper-writing .cursor/skills/paper-writing && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "paper-writing" agent skill from https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writing into .cursor/skills/paper-writing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-writing", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/fcakyon/phd-skills.git --path plugin/skills/paper-writing--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add fcakyon/phd-skills --skill paper-writing -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install fcakyon/phd-skills paper-writing --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/plugin/skills/paper-writing .gemini/skills/paper-writing && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "paper-writing" agent skill from https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writing into .gemini/skills/paper-writing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-writing", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install fcakyon/phd-skills paper-writingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add fcakyon/phd-skills --skill paper-writing -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/plugin/skills/paper-writing .github/skills/paper-writing && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "paper-writing" agent skill from https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writing into .github/skills/paper-writing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-writing", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add fcakyon/phd-skills --skill paper-writing -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install fcakyon/phd-skills paper-writing --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/fcakyon/phd-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/plugin/skills/paper-writing .opencode/skills/paper-writing && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "paper-writing" agent skill from https://github.com/fcakyon/phd-skills/tree/main/plugin/skills/paper-writing into .opencode/skills/paper-writing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-writing", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
paper-writing- GitHub stars
- 415
- Token cost
- ~1.2k tokens
- SKILL.md length
- 595 words
- Files
- 1
- Skills in repo
- 12
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when the user wants to write, structure, or revise academic paper sections, improve notation consistency, or refine figures and tables.
- Works in 4 steps: Specification Capture → Constraint Preservation → Variant Generation → …
- The user wants to write
- SKILL.md covers Core Principles, Section-Specific Guidance, Notation Consistency Protocol and Figure Refinement Methodology, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Paper Writing is an agent skill from fcakyon/phd-skills. Use when the user wants to write, structure, or revise academic paper sections, improve notation consistency, or refine figures and tables. Triggers on phrases like "write the abstract", "structure the methods", "improve this section", "notation consistency", "figure refinement", or "paper structure".
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Scientific writing. The repository describes itself as: PhD Research Skills for Claude Code: paper reproduction, experiment design, paper review, result comparison and more. The licence is MIT.
When your agent uses it
- The user wants to write
- Revise academic paper sections
- Improve notation consistency
- Refine figures and tables
Example prompts
- “write the abstract”
- “structure the methods”
- “improve this section”
- “/paper-writing”
Workflow steps
4 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 67acd61. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Paper Writing loads about 1.2k tokens when it runs. Until then it costs about 79 tokens; SKILL.md has 595 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from fcakyon/phd-skills at commit 67acd61, republished under its MIT licence (© fcakyon). 595 words, ~1,221 tokens.
Download SKILL.mdSave it as
.claude/skills/paper-writing/SKILL.md (or your agent's skills folder).- name
- paper-writing
- description
- Use when the user wants to write, structure, or revise academic paper sections, improve notation consistency, or refine figures and tables. Triggers on phrases like "write the abstract", "structure the methods", "improve this section", "notation consistency", "figure refinement", or "paper structure".
Academic Paper Writing Methodology
You are helping a researcher write or revise an academic paper. Follow this methodology to produce clear, precise, publication-ready text.
Core Principles
- Precision over elegance — every sentence must be verifiable against code or data
- Claims require evidence — never state a result without pointing to its source
- Notation consistency — define once, use identically everywhere
- Conciseness — remove words that don't add information
Section-Specific Guidance
Abstract
- Structure: problem → approach → key result → significance
- Include 1-2 concrete numbers (dataset size, main metric improvement)
- Every number must be traceable to a specific experiment
- No citations in abstract unless venue requires it
Introduction
- Paragraph 1: Problem and why it matters (societal/practical motivation)
- Paragraph 2: Why existing approaches are insufficient (gap)
- Paragraph 3: Your approach and why it addresses the gap
- Paragraph 4: Contributions list (concrete, falsifiable claims)
- Each contribution must map to a section that provides evidence
Related Work
- Organize by theme/approach, not chronologically
- For each group: what they do, what's missing, how your work differs
- Be fair: acknowledge strengths of prior work, don't strawman
- End each paragraph with how your work addresses the limitation
Methods
- Define all notation in a single place (notation table or first-use definitions)
- Each method component should be independently understandable
- Include enough detail that someone could reimplement from the paper
- Cross-reference equations with corresponding code
Experiments
- Dataset: size, splits, preprocessing (cite or describe collection)
- Metrics: define formally, explain why these metrics
- Baselines: justify selection, ensure fair comparison
- Results table: highlight best results, include std dev or CI if available
- Ablations: one factor at a time, clearly show contribution of each component
Conclusion
- Summarize contributions (not the entire paper)
- State limitations honestly
- Future work: specific and feasible, not vague
Notation Consistency Protocol
When writing or editing any section:
- Read existing notation definitions in the paper
- Use EXACTLY the same symbols — do not introduce synonyms
- If a new symbol is needed, check it doesn't clash with existing ones
- Maintain a notation table if the paper has one
Common pitfalls:
- Using both $x$ and $\mathbf{x}$ for the same concept
- Defining $N$ as dataset size in methods but using $n$ in experiments
- Inconsistent subscript conventions (e.g., $f_i$ vs $f(i)$)
Show full SKILL.md (230 more words)Show less
Figure Refinement Methodology
Figures are the most iterated component. Follow this process:
1. Specification Capture
Before generating or modifying any figure:
- What data does it show? (exact source file/variable)
- What message should the reader take away?
- What are the hard constraints? (font size ≥ 8pt, column width, color scheme)
- What aspects of the current version are correct and must be preserved?
2. Constraint Preservation
Across multiple rounds of revision, track constraints explicitly:
Constraints for Figure N:
- [KEEP] Y-axis range 0-100
- [KEEP] Color scheme: blue=ours, gray=baselines
- [CHANGE] Legend position: inside → outside
- [ADD] Error bars from std_results.json3. Variant Generation
When exploring design alternatives:
- Generate 2-3 variants side by side when feasible
- Each variant changes ONE visual aspect
- Let the user compare and choose, don't pick for them
4. Visual Verification
After generating any figure:
- ALWAYS read/inspect the generated image file
- Check that data values match the source
- Verify labels, legends, and annotations are correct
- Confirm the takeaway message is clear from a glance
Writing Process
- Read first — always read the existing section before writing
- Identify the claim — what is this paragraph trying to say?
- Find the evidence — where in code/results does this come from?
- Write the text — state claim, present evidence, interpret
- Verify — re-read against source to catch any drift
Output Format
When writing paper text:
- Provide LaTeX-ready output that matches the paper's existing style
- Include comments for any claim that needs verification:
% TODO: verify this number - Flag any notation inconsistencies found during writing
- Suggest specific improvements with before/after comparisons
© fcakyon, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in plugin/skills/paper-writing of fcakyon/phd-skills.
Open the folder on GitHubat commit 67acd61
Compare with similar skills
Paper Writing next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Paper Writing this skillfcakyon/phd-skills | 415 | — | ~1.2k | Automated safety check: Pass | MIT | |
| Nature-Style Scientific FiguresYuan1z0825/nature-skills | 47k | — | ~2.9k | Automated safety check: Pass | Apache-2.0 | |
| Citation Verification GuideGalaxy-Dawn/claude-scholar | 5.7k | 2 repos | ~1.9k | Automated safety check: Pass | MIT | |
| Citation ManagementK-Dense-AI/claude-scientific-writer | 2.4k | 2 repos | ~3.9k | Automated safety check: Notes | MIT | |
| Academic Paper Composerlishix520/academic-paper-skills | 1.4k | 2 repos | ~6.3k | Automated safety check: Pass | MIT | |
| Academic Paper Writing PipelineImbad0202/academic-research-skills | 51k | — | ~16k | Automated safety check: Pass | Custom licence |
Similar skills
Citation Verification Guide
Galaxy-Dawn/claude-scholar
Reference guidance for checking every citation in academic writing against canonical sources such as DOI, arXiv, CrossRef and Semantic Scholar, to catch fake or wrong references.
Citation Management
K-Dense-AI/claude-scientific-writer
Finds papers in OpenAlex, PubMed and Google Scholar, turns DOIs, PMIDs and arXiv IDs into clean BibTeX, and validates citations for a manuscript or thesis.
Academic Paper Composer
lishix520/academic-paper-skills
Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript.
Academic Paper Writing Pipeline
Imbad0202/academic-research-skills
Runs a 12-agent pipeline that plans, drafts, cites, reviews and formats academic papers, with modes for revision, rebuttals, abstracts and citation checks.
Scientific Venue Templates
davila7/claude-code-templates
Supplies LaTeX templates and formatting rules for journals, conferences, posters, and grant proposals, then can check a draft against them.
More from fcakyon/phd-skills
All 12 skills in this repoReproduce
fcakyon/phd-skills
End-to-end paper reproduction from arxiv URL through smoke runs to replication experiments.
Compare
fcakyon/phd-skills
Same-epoch comparison of training runs across wandb, neptune, tensorboard, or mlflow.
Debug
fcakyon/phd-skills
Evidence-before-action diagnosis of failing ML experiments. An agent skill from fcakyon/phd-skills.
Experiment Design
fcakyon/phd-skills
A skill your agent uses when the user wants to design experiments, plan ablation studies, structure baselines, or create incremental evaluation strategies.
Latex Setup
fcakyon/phd-skills
A skill your agent uses when the user wants to set up or troubleshoot a LaTeX environment, choose between biber and bibtex, install packages for a specific venue template, or configure compilation.
Launch
fcakyon/phd-skills
Pre-flight checklist for long-running ML training jobs covering config diff, run naming, path verification, monitoring setup, and restart-cleanup.
Related
Categories
Questions about Paper Writing
What does Paper Writing do?
A skill your agent uses when the user wants to write, structure, or revise academic paper sections, improve notation consistency, or refine figures and tables. Paper Writing is an agent skill from fcakyon/phd-skills. Use when the user wants to write, structure, or revise academic paper sections, improve notation consistency, or refine figures and tables.
When should I use Paper Writing?
Paper Writing fits situations like: the user wants to write; revise academic paper sections; improve notation consistency; refine figures and tables.
How do I install Paper Writing in Claude Code?
Run `npx skills add fcakyon/phd-skills --skill paper-writing -a claude-code`. Or copy the skill folder (plugin/skills/paper-writing in fcakyon/phd-skills) into .claude/skills/paper-writing in your project. Claude Code loads it when a task matches its description.
How do I install Paper Writing in Codex?
Run `npx skills add fcakyon/phd-skills --skill paper-writing -a codex`. Or copy the skill folder (plugin/skills/paper-writing in fcakyon/phd-skills) into .agents/skills/paper-writing in your project. Codex loads it when a task matches its description.
Can I use Paper Writing in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add fcakyon/phd-skills --skill paper-writing -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/paper-writing, .gemini/skills/paper-writing, .github/skills/paper-writing and .opencode/skills/paper-writing in your project.
What does Paper Writing need to run?
SKILL.md names no scripts, command-line tools or credentials: Paper Writing is instructions for the agent only.
Does Paper Writing access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Paper Writing safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Paper Writing use?
Paper Writing is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Paper Writing use?
About 1.2k tokens (SKILL.md is roughly 4.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Paper Writing?
Skills that share tags, products or a category with Paper Writing: Nature-Style Scientific Figures (Yuan1z0825/nature-skills, 47k stars), Citation Verification Guide (Galaxy-Dawn/claude-scholar, 5.7k stars), Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars) and Academic Paper Composer (lishix520/academic-paper-skills, 1.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Paper Writing?
fcakyon (a GitHub user) maintains it in fcakyon/phd-skills, which has 415 GitHub stars. The repository holds 12 skills in this directory. The repository was last updated on September 16, 2026.
Source: fcakyon/phd-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.