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Bvbrc MCP Server

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BV-BRC MCP Server

A Model Context Protocol (MCP) server for the Bacterial-Viral Bioinformatics Resource Center (BV-BRC):

Data Tools: Query BV-BRC Solr collections for genome, feature, and other biological data
Service Tools: Submit and manage BV-BRC analysis jobs (assembly, annotation, BLAST, etc.)
Workspace Tools: Manage BV-BRC workspace files, folders, and groups

Note: This repository has historically also carried README content for the BV-BRC Copilot API (a separate Node/Express service). That documentation is preserved below under “BV-BRC Copilot API (reference)”.

Features

Data Tools

query_collection: Query any BV-BRC Solr collection with flexible filtering
solr_collection_parameters: Get schema information for collections
solr_query_instructions: Get help on query syntax
solr_collections: List all available collections

Service Tools

list_service_apps: List all available BV-BRC analysis services
get_job_details: Query the status of submitted jobs
Submit jobs for various analyses:
- Genome Assembly
- Genome Annotation
- Comprehensive Genome Analysis
- BLAST
- Primer Design
- Variation Analysis
- TnSeq
- Phylogenetic Trees (Bacterial Genome Tree, Gene Tree)
- SNP Analysis (Whole Genome, MSA)
- Metagenomics (Taxonomic Classification, Binning, Read Mapping)
- RNA-Seq
- Viral Services (SARS-CoV-2 Analysis, Sequence Submission)
- And many more...

Workspace Tools

workspace_browse_tool: Unified browse/search tool (search recursively or inspect path as folder listing/file metadata)
get_file_metadata: Get normalized metadata for workspace files or local session files
workspace_download_file_tool: Download workspace files
workspace_upload: Upload files to workspace
create_genome_group: Create genome groups
create_feature_group: Create feature groups
get_genome_group_ids: Get genome IDs from a group
get_feature_group_ids: Get feature IDs from a group

Connecting the Remote BV-BRC MCP Server to ChatGPT

Step 1: Enable Developer Mode

Click the plus next to "Ask me anything"
Click "Add sources"
You should now see "Sources" and "Add" below your chat box
Click the down arrow next to "Add"
Click "Connect more"
Scroll down to Advanced Settings
Click the toggle next to Developer Mode (must be "on")
Click Back

Step 2: Create MCP Server Connection

In the upper right-hand corner, click "Create"
Fill in the following:
- Icon: Optional
- Name: BV-BRC MCP
- Description: ''
- MCP Server URL: https://dev-7.bv-brc.org/mcp
Authentication:
- Leave authentication on OAuth
Check the box if you Trust this application
Click "Create"

Step 3: Connect to Your Server

You should now see 'BV-BRC MCP' under "Enabled apps & connectors"
Click the 'X' in the top left to go back to the chat screen
In a New Chat, click the '+' button and hover over More

You should see BV-BRC MCP as an option under Canvas

Select BV-BRC MCP

Connecting the Remote BV-BRC MCP Server to Claude

Click account in bottom left and go to settings
Click 'Connectors'
Click 'Add custom connector'
Fill in the following:
- Name: BV-BRC MCP
- Remote MCP server URL: https://dev-7.bv-brc.org/mcp
Click 'Add'
Then click 'Connect'
Log into BV-BRC
It's now available to use in a new chat

Installing as a Claude Extension

Open your terminal

Clone Github Repository

git clone https://github.com/cucinellclark/bvbrc-mcp-server
cd bvbrc-mcp-server