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Agent skill

Pnasnexus Workflow

by brycewang-stanford in brycewang-stanford/Awesome-Journal-Skills

A skill your agent uses when deciding which pnasnexus- sub-skill to invoke next, or when sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully…

MITAuto-check passedResearch & Science

Install Pnasnexus Workflow

skills CLI
$ npx skills add brycewang-stanford/Awesome-Journal-Skills --skill pnasnexus-workflow -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install brycewang-stanford/Awesome-Journal-Skills pnasnexus-workflow --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/brycewang-stanford/Awesome-Journal-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/PNAS-Nexus-Skills/skills/pnasnexus-workflow .claude/skills/pnasnexus-workflow && rm -rf skills-src

Use ~/.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/

Facts

Skill name
pnasnexus-workflow
GitHub stars
1.2k
Token cost
~2.1k tokens
SKILL.md length
895 words
Files
1
Skills in repo
2,387
Repo updated
First seen
Licence
MIT

At a glance

A skill your agent uses when deciding which pnasnexus- sub-skill to invoke next, or when sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully…

  • Works in 11 steps: pnasnexus-fit — clear the… → pnasnexus-openaccess — APC,… → pnasnexus-writing — article type,… → …
  • Deciding which pnasnexus- sub-skill to invoke next
  • SKILL.md covers Overview, When to trigger, The single most important gate and Routing table, plus 5 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Pnasnexus Workflow is an agent skill from brycewang-stanford/Awesome-Journal-Skills. Use when deciding which pnasnexus- sub-skill to invoke next, or when sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully open-access sibling journal of PNAS, published by Oxford University Press for the U.S. National Academy of Sciences). Routes — it does not replace — the specialized skills.

Its SKILL.md is about 2.1k 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. The repository describes itself as: Journal-specific Claude Code/Codex skill packs covering mainstream journals — AER, QJE, Nature, Cell, 管理世界, 经济研究 & 200+ more — your fast track to getting published. ｜ 覆盖主流期刊的… The licence is MIT.

When your agent uses it

  • Deciding which pnasnexus- sub-skill to invoke next
  • Sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully open-access sibling journal of PNAS
  • Published by Oxford University Press for the U.S

Example prompts

  • “/pnasnexus-workflow”

Workflow steps

11 steps, taken from the first numbered list in SKILL.md.

  1. pnasnexus-fit — clear the broad-significance bar; confirm PNAS Nexus is the venue (incl. the PNAS transfer call)
  2. pnasnexus-openaccess — APC, waiver/discount eligibility, license choice (do this early; it gates submission)
  3. pnasnexus-writing — article type, structure, classification, in-text Methods, page budget
  4. pnasnexus-figures — finalize display items within the graphical-element budget
  5. pnasnexus-statistics — rigor & reproducibility (and whether a Registered Report fits)
  6. pnasnexus-data — mandatory data/code deposition + raw-image retention
  7. pnasnexus-significance — the 50–120-word Significance Statement (high-value; draft early)
  8. pnasnexus-abstract — ≤250-word single-paragraph abstract (late polish)
  9. pnasnexus-citation — references (format-neutral at submission; make them clean and consistent)
  10. pnasnexus-submission — preflight + cover letter
  11. pnasnexus-rebuttal — after review

What it can do on your machine

Read from SKILL.md and the folder at commit 932eb23. 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

Pnasnexus Workflow loads about 2.1k tokens when it runs. Until then it costs about 92 tokens; SKILL.md has 895 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~92
When it runs · the whole SKILL.md, loaded when a task matches
~2.1k

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 brycewang-stanford/Awesome-Journal-Skills at commit 932eb23, republished under its MIT licence (© brycewang-stanford). 895 words, ~2,112 tokens.

Download SKILL.mdSave it as .claude/skills/pnasnexus-workflow/SKILL.md (or your agent's skills folder).
name
pnasnexus-workflow
description
Use when deciding which pnasnexus-* sub-skill to invoke next, or when sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully open-access sibling journal of PNAS, published by Oxford University Press for the U.S. National Academy of Sciences). Routes — it does not replace — the specialized skills.

PNAS Nexus Workflow Router (pnasnexus-workflow)

Overview

This is the router. It does not replace any specialized skill. It tells you which pnasnexus- skill to use at the current stage* of a manuscript aimed at PNAS Nexus.

PNAS Nexus is not flagship PNAS. It is the gold open-access sibling journal, published by Oxford University Press (OUP) in partnership with the National Academy of Sciences (NAS). Two things reshape the workflow relative to the pnas-skills pack and must be settled early: (1) it is fully open access with an article processing charge (APC) and a CC BY / CC BY-NC license choice (pnasnexus-openaccess), and (2) it has no Direct/Contributed submission track — every paper goes through standard editor-assigned peer review. PNAS Nexus also has a transfer route from flagship PNAS that carries reviews over (pnasnexus-fit).

When to trigger

  • "What should I do next with this draft?"
  • A draft arrives and you must diagnose the current bottleneck.
  • The user just had a paper declined by PNAS and is considering the PNAS Nexus transfer.
  • The user is unsure about open-access cost, waivers, or which license to pick.
  • Reviews arrive from PNAS Nexus and you need to switch into rebuttal mode.

The single most important gate

Route to pnasnexus-fit first, always. The first question is "is this high-quality, broadly significant, multidisciplinary research that the PNAS Nexus readership across biological/health/medical, physical sciences & engineering, and social & political sciences would value?" PNAS Nexus is positioned as a complementary, broad-scope sibling to PNAS — including via a transfer route for sound work declined at PNAS — so pnasnexus-fit also handles the "we were declined at PNAS, is the transfer right?" decision.

Settle open access early. Because every PNAS Nexus article is OA and carries an APC, confirm funding, eligibility for a waiver/discount, and license choice before you invest in polishing — run pnasnexus-openaccess right after pnasnexus-fit.

Routing table

Current symptomNext skill
Not sure the result fits PNAS Nexus, or deciding whether to transfer from PNASpnasnexus-fit
Unsure about the APC, waivers/discounts, license (CC BY vs CC BY-NC), or funder compliancepnasnexus-openaccess
No Significance Statement, or it is outside 50–120 words / just restates the abstractpnasnexus-significance
Abstract too long/narrow, has headings, or conflated with the significance statementpnasnexus-abstract
Unsure of article type; structure unclear; Methods misplaced; over the page budget; no classificationpnasnexus-writing
Figures/tables over the graphical-element budget; sizing/fonts/colors non-compliantpnasnexus-figures
Stats under-reported; n/error bars/tests unclear; not reproducible; considering a Registered Reportpnasnexus-statistics
No data/code deposition plan; raw images not retained; "on request" onlypnasnexus-data
References messy/inconsistent (note: format-neutral at submission)pnasnexus-citation
About to submit; need a preflight checklist + cover letterpnasnexus-submission
Received reviews / a revision decisionpnasnexus-rebuttal

Default order

  1. pnasnexus-fit — clear the broad-significance bar; confirm PNAS Nexus is the venue (incl. the PNAS transfer call)
  2. pnasnexus-openaccess — APC, waiver/discount eligibility, license choice (do this early; it gates submission)
  3. pnasnexus-writing — article type, structure, classification, in-text Methods, page budget
  4. pnasnexus-figures — finalize display items within the graphical-element budget
  5. pnasnexus-statistics — rigor & reproducibility (and whether a Registered Report fits)
  6. pnasnexus-data — mandatory data/code deposition + raw-image retention
  7. pnasnexus-significance — the 50–120-word Significance Statement (high-value; draft early)
  8. pnasnexus-abstract — ≤250-word single-paragraph abstract (late polish)
  9. pnasnexus-citation — references (format-neutral at submission; make them clean and consistent)
  10. pnasnexus-submission — preflight + cover letter
  11. pnasnexus-rebuttal — after review

pnasnexus-significance, pnasnexus-abstract, and pnasnexus-citation are late-stage polish — but the Significance Statement is high-value and editor-facing, so draft it as soon as the claim is locked.

Show full SKILL.md (332 more words)Show less

Manuscript state ledger

Keep one ledger per manuscript and update it after every routing decision. The two early gates (fit and open access) are binary and block everything downstream; the rest are progress fields.

text
PNAS NEXUS ROUTE LEDGER
manuscript: __________________   date: __________
[gate] fit verdict ........ in-scope / transfer-from-PNAS / wrong venue
[gate] APC funding ........ confirmed / waiver-discount pending / unresolved
[gate] license ............ CC BY / CC BY-NC (funder-compatible? Y/N)
article type .............. Research Report / Brief Report / Perspective /
                            Review / Registered Report
page budget ............... current ___ pp vs type budget (Methods in main text)
graphical elements ........ ___ used / budget for type
significance statement .... drafted (50-120 words) Y/N
abstract .................. single paragraph, <=250 words Y/N
data + code deposition .... repository chosen + raw images retained Y/N
references ................ internally consistent (style-neutral at submission)
next skill ................ pnasnexus-______

Decision shortcuts

  • "PNAS declined us — should we accept the PNAS Nexus transfer?" → pnasnexus-fit
  • "How much will open access cost, and can we get a waiver?" → pnasnexus-openaccess
  • "Which license — CC BY or CC BY-NC?" → pnasnexus-openaccess
  • "Is a co-author who is an NAS member able to 'contribute' this paper?" → pnasnexus-openaccess / pnasnexus-fit (no — PNAS Nexus has no Contributed track)
  • "What article type is this — Research Report, Brief Report, Perspective, Review?" → pnasnexus-writing
  • "Where do Materials and Methods go?" → pnasnexus-writing (in the main text)
  • "Do I really have to deposit the data and code?" → pnasnexus-data (yes — mandatory, with retraction teeth)

How PNAS Nexus differs from flagship PNAS (do not transcribe PNAS facts here)

  • Business model: PNAS Nexus is fully gold open access with an APC; flagship PNAS is hybrid. Cost, waivers, and license choice are real workflow steps here (pnasnexus-openaccess).
  • No submission tracks: PNAS Nexus has no Direct vs Contributed (NAS-member) choice — all editor-assigned peer review. The pnas-track skill has no equivalent; its slot is taken by pnasnexus-openaccess.
  • Transfer route in: sound work declined by PNAS can be transferred to PNAS Nexus with reviews carried over (pnasnexus-fit).
  • Scope & board: broader, explicitly cross-disciplinary; the editorial board spans the NAS, NAE, and NAM.
  • Length: page-based budgets and named article types (Research Report ≈6 pp / 12 max, Brief Report, Perspective, Review, Registered Reports) — pnasnexus-writing.
  • References: format-neutral at submission — not the strict numbered-by-appearance PNAS demands up front (pnasnexus-citation).
  • Significance Statement: 50–120 words (note the minimum) (pnasnexus-significance).

Anti-patterns

  • Do not skip pnasnexus-fit and start polishing prose.
  • Do not defer the open-access/APC/license decision to the final upload — it gates submission (pnasnexus-openaccess).
  • Do not assume a Direct/Contributed track exists — it does not.
  • Do not copy length, reference-style, or fee facts from the flagship pnas-skills pack; PNAS Nexus differs.
  • Do not generate a rebuttal before the main text is actually revised.

© brycewang-stanford, 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 PNAS-Nexus-Skills/skills/pnasnexus-workflow of brycewang-stanford/Awesome-Journal-Skills.

Open the folder on GitHubat commit 932eb23

Compare with similar skills

Pnasnexus Workflow 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.

Pnasnexus Workflow compared with similar skills
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Nature Paper CardYuan1z0825/nature-skills47k2 repos~2.1kAutomated safety check: PassApache-2.0
Content Research Writerweapp-tailwindcss/weapp-tailwindcss1.9k25 repos~3.5kAutomated safety check: PassMIT
Last30daysmvanhorn/last30days-skill64k—~7.9kAutomated safety check: NotesMIT

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Categories

Questions about Pnasnexus Workflow

What does Pnasnexus Workflow do?

A skill your agent uses when deciding which pnasnexus- sub-skill to invoke next, or when sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully…. Pnasnexus Workflow is an agent skill from brycewang-stanford/Awesome-Journal-Skills.S.

When should I use Pnasnexus Workflow?

Pnasnexus Workflow fits situations like: deciding which pnasnexus- sub-skill to invoke next; sequencing a manuscript from scope/significance test through reviewer rebuttal for PNAS Nexus (the fully open-access sibling journal of PNAS; published by Oxford University Press for the U.S.

How do I install Pnasnexus Workflow in Claude Code?

Run `npx skills add brycewang-stanford/Awesome-Journal-Skills --skill pnasnexus-workflow -a claude-code`. Or copy the skill folder (PNAS-Nexus-Skills/skills/pnasnexus-workflow in brycewang-stanford/Awesome-Journal-Skills) into .claude/skills/pnasnexus-workflow in your project. Claude Code loads it when a task matches its description.

How do I install Pnasnexus Workflow in Codex?

Run `npx skills add brycewang-stanford/Awesome-Journal-Skills --skill pnasnexus-workflow -a codex`. Or copy the skill folder (PNAS-Nexus-Skills/skills/pnasnexus-workflow in brycewang-stanford/Awesome-Journal-Skills) into .agents/skills/pnasnexus-workflow in your project. Codex loads it when a task matches its description.

Can I use Pnasnexus Workflow 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 brycewang-stanford/Awesome-Journal-Skills --skill pnasnexus-workflow -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pnasnexus-workflow, .gemini/skills/pnasnexus-workflow, .github/skills/pnasnexus-workflow and .opencode/skills/pnasnexus-workflow in your project.

What does Pnasnexus Workflow need to run?

SKILL.md names no scripts, command-line tools or credentials: Pnasnexus Workflow is instructions for the agent only.

Does Pnasnexus Workflow 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 Pnasnexus Workflow 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 Pnasnexus Workflow use?

Pnasnexus Workflow 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 Pnasnexus Workflow use?

About 2.1k tokens (SKILL.md is roughly 8.4k 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 Pnasnexus Workflow?

Skills that share tags, products or a category with Pnasnexus Workflow: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pnasnexus Workflow?

brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Awesome-Journal-Skills, which has 1,231 GitHub stars. The repository holds 2,387 skills in this directory. The repository was last updated on September 27, 2026.

Source: brycewang-stanford/Awesome-Journal-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.