Stanford bioRxiv MCP Server for LlamaIndexGive LlamaIndex instant access to 16 tools to Get Preprint, Get Preprint Versions, Get Published Tracking, and more
GDPR Free for SubscribersLlamaIndex specializes in data-aware AI agents that connect LLMs to structured and unstructured sources. Add Stanford bioRxiv as an MCP tool provider through Vinkius and your agents can query, analyze, and act on live data alongside your existing indexes.
Ask AI about this MCP Server for LlamaIndex
The Stanford bioRxiv MCP Server for LlamaIndex is a standout in the Education category — giving your AI agent 16 tools to work with, ready to go from day one.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Geminiimport asyncio
from llama_index.tools.mcp import BasicMCPClient, McpToolSpec
from llama_index.core.agent.workflow import FunctionAgent
from llama_index.llms.openai import OpenAI
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
mcp_client = BasicMCPClient("https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")
mcp_tool_spec = McpToolSpec(client=mcp_client)
tools = await mcp_tool_spec.to_tool_list_async()
agent = FunctionAgent(
tools=tools,
llm=OpenAI(model="gpt-4o"),
system_prompt=(
"You are an assistant with access to Stanford bioRxiv. "
"You have 16 tools available."
),
)
response = await agent.run(
"What tools are available in Stanford bioRxiv?"
)
print(response)
asyncio.run(main())
* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
About Stanford bioRxiv MCP Server
Connect to the bioRxiv and medRxiv APIs — the world's leading preprint servers for biology and health sciences.
LlamaIndex agents combine Stanford bioRxiv tool responses with indexed documents for comprehensive, grounded answers. Connect 16 tools through Vinkius and query live data alongside vector stores and SQL databases in a single turn. ideal for hybrid search, data enrichment, and analytical workflows.
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 LlamaIndex 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 LlamaIndex
When LlamaIndex 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 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 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 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 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 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 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 LlamaIndex via MCP
Follow these steps to wire Stanford bioRxiv into LlamaIndex. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install dependencies
pip install llama-index-tools-mcp llama-index-llms-openaiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenRun the agent
agent.py and run: python agent.pyExplore tools
Why Use LlamaIndex with the Stanford bioRxiv MCP Server
LlamaIndex provides unique advantages when paired with Stanford bioRxiv through the Model Context Protocol.
Data-first architecture: LlamaIndex agents combine Stanford bioRxiv tool responses with indexed documents for comprehensive, grounded answers
Query pipeline framework lets you chain Stanford bioRxiv tool calls with transformations, filters, and re-rankers in a typed pipeline
Multi-source reasoning: agents can query Stanford bioRxiv, a vector store, and a SQL database in a single turn and synthesize results
Observability integrations show exactly what Stanford bioRxiv tools were called, what data was returned, and how it influenced the final answer
Stanford bioRxiv + LlamaIndex Use Cases
Practical scenarios where LlamaIndex combined with the Stanford bioRxiv MCP Server delivers measurable value.
Hybrid search: combine Stanford bioRxiv real-time data with embedded document indexes for answers that are both current and comprehensive
Data enrichment: query Stanford bioRxiv to augment indexed data with live information before generating user-facing responses
Knowledge base agents: build agents that maintain and update knowledge bases by periodically querying Stanford bioRxiv for fresh data
Analytical workflows: chain Stanford bioRxiv queries with LlamaIndex's data connectors to build multi-source analytical reports
Example Prompts for Stanford bioRxiv in LlamaIndex
Ready-to-use prompts you can give your LlamaIndex 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 LlamaIndex
Common issues when connecting Stanford bioRxiv to LlamaIndex through Vinkius, and how to resolve them.
BasicMCPClient not found
pip install llama-index-tools-mcpStanford bioRxiv + LlamaIndex FAQ
Common questions about integrating Stanford bioRxiv MCP Server with LlamaIndex.
How does LlamaIndex connect to MCP servers?
Can I combine MCP tools with vector stores?
Does LlamaIndex support async MCP calls?
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