manuscript-optimizer

manuscript-optimizer is a skill for Claude Code, Codex from Boom5426/Nature-Paper-Skills. It costs 85 tokens per session (3,265 once invoked), scanned A, original, MIT.

A skill for reviewing and restructuring research manuscripts when the scientific question, claims, evidence, sections, figures, terminology, or wording do not line up clearly. It treats the manuscript as a chain of reasoning rather than only a piece of prose.

In plain words
What is it for?
Use it to audit a full research draft, reorganize major sections, align figures with the text, reduce overclaiming, and prepare a manuscript for clearer revision.
Why use it?
It helps fix unsupported claims, missing links between evidence and conclusions, and confusing organization before sentence-level editing. It prioritizes scientific accuracy and logic over style.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it to audit a full research draft, reorganize major sections, align figures with the text, reduce overclaiming, and prepare a manuscript for clearer revision.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/boom5426/nature-paper-skills/manuscript-optimizer
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Boom5426/Nature-Paper-Skills --skill manuscript-optimizer
Clone the repo
git clone --depth 1 https://github.com/Boom5426/Nature-Paper-Skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for manuscript-optimizer

README.md
[![agentmods](https://agentmods.dev/badge/skills/boom5426/nature-paper-skills/manuscript-optimizer/github.svg)](https://agentmods.dev/skills/boom5426/nature-paper-skills/manuscript-optimizer)
Your own site
<a href="https://agentmods.dev/skills/boom5426/nature-paper-skills/manuscript-optimizer"><img src="https://agentmods.dev/badge/skills/boom5426/nature-paper-skills/manuscript-optimizer/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for manuscript-optimizer

Your own site · 80×15
<a href="https://agentmods.dev/skills/boom5426/nature-paper-skills/manuscript-optimizer"><img src="https://agentmods.dev/badge/skills/boom5426/nature-paper-skills/manuscript-optimizer.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 85 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,265 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00085 $0.03265
Opus 5 $0.00043 $0.01632
Sonnet 5 $0.00017 $0.00653
Haiku 4.5 $0.00009 $0.00327

Measured 12d ago against content hash 97015ca99358, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

manuscript-optimizer scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/core/manuscript-optimizer/SKILL.md · 364 lines

How it starts

The opening of the file, as written. The whole thing — 364 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Manuscript Optimizer

Treat scientific writing as reasoning, not decoration. Do not make existing results sound more impressive. Organize the scientific question, evidence, interpretation, and conclusion into a chain that a broad scientific reader can follow and evaluate.

Use this priority order without exception:

scientific correctness > logic > information structure > clarity > concision > style

Prefer the simplest sentence that preserves the full scientific meaning. Never polish prose built on an unstable claim, a missing evidence link, or a false scientific premise.

Scope and handoff

Use this skill above the sentence level. Own the paper's scientific direction, claim architecture, evidence boundaries, section and paragraph functions, figure-text logic, and terminology.

  • Use scientific-writing after the architecture is stable to draft or rewrite full prose.
  • Use write-scientific-manuscript to repair paragraph-level clarity and local reasoning.
  • Use scientific-prose-style last for punctuation and rhythm.
  • Use results-section-revision only when the claims are stable and Results needs local flow repair.
  • Use review-article-architecture instead for a Review, survey, or Perspective.

For review-only requests, diagnose and stop. For revision requests, diagnose first and then edit in the macro-to-micro order below.

Hard constraints

Preserve the scientific record. Never:

  • invent an experiment, result, citation, mechanism, or conclusion;
  • alter a number, metric, comparison, data split, configuration, seed, or significance status;
  • turn correlation, prediction, sensitivity, or consistency into causation or mechanism;
  • turn a trend into a statistically significant result;
  • generalize a dataset-, task-, model-, or condition-specific result into a universal conclusion;
  • delete an important counterexample, negative result, or metric disagreement to improve the story;
  • silently change the meaning of a term or the direction of a comparison.

Read the full file on GitHub · 364 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 12d ago First seen · 364 lines · 85 tokens per session scan A 97015ca99358

Subscribe to this mod's changes

manuscript-optimizer is a skill published in the GitHub repository Boom5426/Nature-Paper-Skills (489 stars, last pushed 6d ago), licensed MIT. It adds 85 tokens to every session and 3,265 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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