Biorxiv

Organization

ai4protein

biorxiv

bioRxiv & medRxiv — biology / medicine preprint servers. Search by keyword + date window, fetch a specific preprint's full metadata (with all version history + abstract + JATS XML link) by DOI. Use for cutting-edge biology/medicine work that hasn't gone through peer review yet, or to find the original preprint version of a paper you only have the DOI for.

Overview

Publisher	ai4protein
Repository	`VenusFactory2`
Skill name	`biorxiv`
Stars	255
Forks	37
Bundled files	Instructions only
Links	Skill source Repository Homepage

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by ai4protein on GitHub. Read the source before you install it.

Installation

Install the Biorxiv AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/ai4protein/VenusFactory2/tree/main/src/agent/skills/biorxiv
Enable the skill in any chat where you want it available.

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/ai4protein/VenusFactory2.git /tmp/VenusFactory2
mkdir -p .claude/skills
cp -r /tmp/VenusFactory2/src/agent/skills/biorxiv .claude/skills/biorxiv

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Biorxiv in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Biorxiv on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Biorxiv is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

bioRxiv & medRxiv

Overview

Two tools: existing query_biorxiv_tool (keyword/category date-window search) + new download_biorxiv_by_doi (fetch one preprint by DOI with all metadata, including version history).

Project Tools (VenusFactory2)

Tool	Args	Returns	Description
query_biorxiv	`query` (category or keyword), `max_results` (default 5, max 50), `days` (default 30; date window)	JSON list of paper records inline	Browse recent preprints in a category.
download_biorxiv_by_doi	`doi` (bare `10.1101/...` or DOI URL), `out_dir`, `server` (`biorxiv` \| `medrxiv`; default `biorxiv`), `include_abstract` (default True), `timeout` (default 30s)	rich JSON envelope; full metadata + version list at `file_info.file_path`; `biological_metadata` extracts title/authors/date/category/license/jatsxml URL	Fetch one preprint by DOI.

When to Use Each

Goal	Tool
"Latest bioinformatics preprints"	`query_biorxiv(query="bioinformatics", days=7)`
"Get me preprint X by DOI"	`download_biorxiv_by_doi`
Resolve a published paper back to its preprint version	`download_biorxiv_by_doi(doi=<published-DOI>)` (if a preprint exists with that DOI)
Get JATS XML for ML training data	`download_biorxiv_by_doi`, then GET the `jatsxml` URL from the metadata

Server Choice

biorxiv (default) — biology preprints (>200K papers, since 2013)
medrxiv — medicine / health-sciences preprints (>40K papers, since 2019)

If a DOI isn't found on biorxiv, try medrxiv (they share 10.1101/ DOI prefix).

Version Handling

download_biorxiv_by_doi returns all versions in latest_versions[*]. The top-level latest field is the most recent version (newest version number). Use latest.jatsxml for full-text XML, latest.date for publication date.

Common Mistakes

Wrong server: if you get NotFound, try server="medrxiv" (or vice versa).
DOI URL not normalized: the tool strips https://doi.org/, http://doi.org/, doi: prefixes — fine to paste a URL.
Trying to download the PDF directly: this tool returns the metadata JSON (which includes a PDF URL). To download the PDF, follow the URL via WebFetch or requests.
Old DOI on a withdrawn preprint: the API may still return metadata with type="withdrawn". Check category / type fields if integrity matters.

Frequently asked questions

What does the Biorxiv AI skill do?

Why use Biorxiv on TypingMind?

Because you install it once and use it with any model. Biorxiv is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Biorxiv in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/ai4protein/VenusFactory2/tree/main/src/agent/skills/biorxiv. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Biorxiv?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Biorxiv?

As many as you like. As long as a model supports skills, you can use Biorxiv with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Biorxiv AI skill free?

It is published on GitHub by ai4protein. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

bioRxiv & medRxiv

Overview

Project Tools (VenusFactory2)

When to Use Each

Server Choice

Version Handling

Common Mistakes

References

Frequently asked questions

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