biorxiv-database

biorxiv-database is a skill for Claude Code, Codex from nevergoodstudy-hub/wechat-article-summarizer. It costs 52 tokens per session (3,174 once invoked), scanned A, a copy of biorxiv-database, MIT.

A search and retrieval tool for bioRxiv, a website where life-science researchers share papers before formal journal review.

In plain words
What is it for?
It is for keyword, author, date, and subject searches, literature reviews, trend analysis, citation metadata, and PDF retrieval.
Why use it?
It reduces the work of finding relevant preprints and collecting their details or full PDFs.

Skill for Claude CodeCodex

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

Needs its repository: it runs a file that does not travel with it, so clone the repository first. The line is python tests/test_biorxiv_search.py.

Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo
git clone --depth 1 https://github.com/nevergoodstudy-hub/wechat-article-summarizer
agentmods
npx agentmods add skills/nevergoodstudy-hub/wechat-article-summarizer/biorxiv-database

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 biorxiv-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/nevergoodstudy-hub/wechat-article-summarizer/biorxiv-database.svg)](https://agentmods.dev/skills/nevergoodstudy-hub/wechat-article-summarizer/biorxiv-database)
Your own site
<a href="https://agentmods.dev/skills/nevergoodstudy-hub/wechat-article-summarizer/biorxiv-database"><img src="https://agentmods.dev/badge/skills/nevergoodstudy-hub/wechat-article-summarizer/biorxiv-database.svg" alt="Measured on agentmods" height="20"></a>
Per session 52 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,174 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin 97% copy Near-identical to another mod 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 $0.00052 $0.03174
Opus 5 $0.00026 $0.01587
Sonnet 5 $0.00010 $0.00635
Haiku 4.5 $0.00005 $0.00317

Measured 2d ago against content hash ea38a1d2b044, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-06, from the pricing page.

Security

Grade A, and why

biorxiv-database 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 2d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/biorxiv_search.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Origin

This is a copy

97% identical to biorxiv-database — 3 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

.warp/skills/biorxiv-database/SKILL.md · 482 lines

How it starts

The opening of the file, as written. The whole thing — 482 lines — stays where its author put it; the contents beside it link to each section on GitHub.

bioRxiv Database

Overview

This skill provides efficient Python-based tools for searching and retrieving preprints from the bioRxiv database. It enables comprehensive searches by keywords, authors, date ranges, and categories, returning structured JSON metadata that includes titles, abstracts, DOIs, and citation information. The skill also supports PDF downloads for full-text analysis.

When to Use This Skill

Use this skill when:

  • Searching for recent preprints in specific research areas
  • Tracking publications by particular authors
  • Conducting systematic literature reviews
  • Analyzing research trends over time periods
  • Retrieving metadata for citation management
  • Downloading preprint PDFs for analysis
  • Filtering papers by bioRxiv subject categories

Core Search Capabilities

1. Keyword Search

Search for preprints containing specific keywords in titles, abstracts, or author lists.

Basic Usage:

python scripts/biorxiv_search.py \
  --keywords "CRISPR" "gene editing" \
  --start-date 2024-01-01 \
  --end-date 2024-12-31 \
  --output results.json

With Category Filter:

python scripts/biorxiv_search.py \
  --keywords "neural networks" "deep learning" \
  --days-back 180 \
  --category neuroscience \
  --output recent_neuroscience.json

Search Fields: By default, keywords are searched in both title and abstract. Customize with --search-fields:

python scripts/biorxiv_search.py \
  --keywords "AlphaFold" \
  --search-fields title \
  --days-back 365

2. Author Search

Find all papers by a specific author within a date range.

Basic Usage:

python scripts/biorxiv_search.py \
  --author "Smith" \
  --start-date 2023-01-01 \
  --end-date 2024-12-31 \
  --output smith_papers.json

Recent Publications:

# Last year by default if no dates specified
python scripts/biorxiv_search.py \
  --author "Johnson" \
  --output johnson_recent.json

3. Date Range Search

Retrieve all preprints posted within a specific date range.

Read the full file on GitHub · 482 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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. 2d ago First seen · 482 lines · 52 tokens per session scan A ea38a1d2b044

Subscribe to this mod's changes

biorxiv-database is a skill published in the GitHub repository nevergoodstudy-hub/wechat-article-summarizer (5 stars, last pushed 2mo ago), licensed MIT. It adds 52 tokens to every session and 3,174 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 97% identical to biorxiv-database, differing in 3 lines, and is treated as a copy.

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