Stanford bioRxiv MCP Server for AutoGenGive AutoGen instant access to 16 tools to Get Preprint, Get Preprint Versions, Get Published Tracking, and more

Name: Stanford bioRxiv
Price: 29 USD
Availability: InStock
Rating: 0.2 (1 reviews)
Author: Vinkius

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Microsoft AutoGen enables multi-agent conversations where agents negotiate, delegate, and execute tasks collaboratively. Add Stanford bioRxiv as an MCP tool provider through Vinkius and every agent in the group can access live data and take action.

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The Stanford bioRxiv MCP Server for AutoGen is a standout in the Education category — giving your AI agent 16 tools to work with, ready to go from day one.

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python

import asyncio
from autogen_agentchat.agents import AssistantAgent
from autogen_ext.tools.mcp import McpWorkbench

async def main():
    # Your Vinkius token. get it at cloud.vinkius.com
    async with McpWorkbench(
        server_params={"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"},
        transport="streamable_http",
    ) as workbench:
        tools = await workbench.list_tools()
        agent = AssistantAgent(
            name="stanford_biorxiv_agent",
            tools=tools,
            system_message=(
                "You help users with Stanford bioRxiv. "
                "16 tools available."
            ),
        )
        print(f"Agent ready with {len(tools)} tools")

asyncio.run(main())

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About Stanford bioRxiv MCP Server

Connect to the bioRxiv and medRxiv APIs — the world's leading preprint servers for biology and health sciences.

AutoGen enables multi-agent conversations where agents negotiate, delegate, and collaboratively use Stanford bioRxiv tools. Connect 16 tools through Vinkius and assign role-based access. a data analyst queries while a reviewer validates, with optional human-in-the-loop approval for sensitive operations.

What you can do

bioRxiv Preprints — Browse the latest biology preprints across 25+ categories
medRxiv Preprints — Browse health sciences preprints (clinical, epidemiology, public health)
Category Filters — Neuroscience, genomics, cell biology, cancer, immunology, and more
Preprint Details — Get full metadata including abstracts by DOI
Version Tracking — See how a preprint has been revised over time
Publication Tracking — Discover which preprints have been published in peer-reviewed journals
Institution View — Browse preprints by corresponding author institution
Subject Feeds — Dedicated feeds for neuroscience, genomics, immunology, cell biology, cancer, and epidemiology

Why preprints matter

Preprints appear 6-12 months before peer-reviewed publication. This server gives you access to science at the cutting edge — the same day researchers share their findings with the world.

The Stanford bioRxiv MCP Server exposes 16 tools through the Vinkius. Connect it to AutoGen in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

All 16 Stanford bioRxiv tools available for AutoGen

When AutoGen connects to Stanford bioRxiv through Vinkius, your AI agent gets direct access to every tool listed below — spanning biorxiv, medrxiv, preprints, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.

get

Get preprint on Stanford bioRxiv

Searches both bioRxiv and medRxiv. Returns title, authors, corresponding author and institution, date, version, category, abstract, and license. DOI format: "10.1101/2024.01.15.575123". Get preprint details by DOI

get

Get preprint versions on Stanford bioRxiv

Preprints on bioRxiv/medRxiv can be updated multiple times. This lets you see the full revision history and understand how a manuscript has evolved. Get all versions of a preprint to track revisions

get

Get published tracking on Stanford bioRxiv

Shows the preprint DOI, published DOI, journal name, and publication date. Essential for understanding the preprint-to-publication pipeline. Track which preprints have been published in journals

get

Get published version on Stanford bioRxiv

Returns the published DOI, journal citation, and publication date. Essential for finding the final, peer-reviewed version of a preprint you have read. Find the journal-published version of a preprint

get

Get recent biorxiv on Stanford bioRxiv

Default is 7 days. Essential for staying at the cutting edge of biological research — preprints appear here 6-12 months before peer-reviewed publication. Get the latest bioRxiv preprints

get

Get recent medrxiv on Stanford bioRxiv

Covers clinical medicine, epidemiology, public health, and health systems research. Critical for monitoring emerging health research before journal publication. Get the latest medRxiv preprints

Search biorxiv on Stanford bioRxiv

The bioRxiv API returns preprints in batches of 100. Use the date interval format "YYYY-MM-DD/YYYY-MM-DD" (e.g. "2024-01-01/2024-01-31"). Use cursor for pagination (0, 100, 200, etc.). Browse bioRxiv preprints by date range

Search by category on Stanford bioRxiv

bioRxiv categories include: neuroscience, genomics, bioinformatics, cell_biology, cancer_biology, immunology, microbiology, molecular_biology, biochemistry, genetics, developmental_biology, evolutionary_biology, ecology, plant_biology, physiology, pharmacology, systems_biology, biophysics, synthetic_biology. medRxiv categories: epidemiology, infectious_diseases, public_and_global_health, health_systems, cardiovascular_medicine, oncology, psychiatry, neurology. Filter preprints by subject category

Search by institution on Stanford bioRxiv

Use this to explore what institutions are producing preprints in a given time period. Each preprint includes the corresponding author and their institutional affiliation. Browse preprints with author institution metadata

Search cancer on Stanford bioRxiv

Covers tumor biology, oncogenomics, cancer immunology, drug resistance, and experimental therapeutics. Browse cancer biology preprints

Search cell biology on Stanford bioRxiv

Covers cell signaling, organelle biology, cytoskeleton, cell division, stem cells, and cellular mechanisms of disease. Browse cell biology preprints

Search epidemiology on Stanford bioRxiv

Covers disease surveillance, outbreak analysis, population health, health policy, and clinical epidemiology. Critical for public health monitoring. Browse epidemiology and public health preprints

Search genomics on Stanford bioRxiv

Covers genome sequencing, gene regulation, epigenomics, metagenomics, and computational genomics — core disciplines in modern biology. Browse genomics and bioinformatics preprints

Search immunology on Stanford bioRxiv

Covers immune system research, host-pathogen interactions, vaccine development, autoimmune diseases, and immunotherapy. Browse immunology and microbiology preprints

Search medrxiv on Stanford bioRxiv

medRxiv covers clinical research, epidemiology, public health, and health policy. Use interval "YYYY-MM-DD/YYYY-MM-DD" format. Results paginated in batches of 100. Browse medRxiv preprints by date range

Search neuroscience on Stanford bioRxiv

Neuroscience is one of the largest and most active categories, covering brain research, neural circuits, cognitive science, and neurological disorders. Browse neuroscience preprints

Connect Stanford bioRxiv to AutoGen via MCP

Follow these steps to wire Stanford bioRxiv into AutoGen. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Install AutoGen

Run pip install "autogen-ext[mcp]"

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token

Integrate into workflow

Use the agent in your AutoGen multi-agent orchestration

Explore tools

The workbench discovers 16 tools from Stanford bioRxiv automatically

Why Use AutoGen with the Stanford bioRxiv MCP Server

AutoGen provides unique advantages when paired with Stanford bioRxiv through the Model Context Protocol.

Multi-agent conversations: multiple AutoGen agents discuss, delegate, and collaboratively use Stanford bioRxiv tools to solve complex tasks

Role-based architecture lets you assign Stanford bioRxiv tool access to specific agents. a data analyst queries while a reviewer validates

Human-in-the-loop support: agents can pause for human approval before executing sensitive Stanford bioRxiv tool calls

Code execution sandbox: AutoGen agents can write and run code that processes Stanford bioRxiv tool responses in an isolated environment

Stanford bioRxiv + AutoGen Use Cases

Practical scenarios where AutoGen combined with the Stanford bioRxiv MCP Server delivers measurable value.

Collaborative analysis: one agent queries Stanford bioRxiv while another validates results and a third generates the final report

Automated review pipelines: a researcher agent fetches data from Stanford bioRxiv, a critic agent evaluates quality, and a writer produces the output

Interactive planning: agents negotiate task allocation using Stanford bioRxiv data to make informed decisions about resource distribution

Code generation with live data: an AutoGen coder agent writes scripts that process Stanford bioRxiv responses in a sandboxed execution environment

Example Prompts for Stanford bioRxiv in AutoGen

Ready-to-use prompts you can give your AutoGen agent to start working with Stanford bioRxiv immediately.

"Show me the latest neuroscience preprints"

"Has preprint 10.1101/2024.01.15.575123 been published in a journal?"

"Find the latest genomics preprints from this week"

Troubleshooting Stanford bioRxiv MCP Server with AutoGen

Common issues when connecting Stanford bioRxiv to AutoGen through Vinkius, and how to resolve them.

McpWorkbench not found

Install: pip install "autogen-ext[mcp]"

Stanford bioRxiv + AutoGen FAQ

Common questions about integrating Stanford bioRxiv MCP Server with AutoGen.

How does AutoGen connect to MCP servers?

Create an MCP tool adapter and assign it to one or more agents in the group chat. AutoGen agents can then call Stanford bioRxiv tools during their conversation turns.

Can different agents have different MCP tool access?

Yes. AutoGen's role-based architecture lets you assign specific MCP tools to specific agents, so a querying agent has different capabilities than a reviewing agent.