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)”.

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

Step 1: Enable Developer Mode

1. Click the plus next to "Ask me anything"

2. Click "Add sources"

3. You should now see "Sources" and "Add" below your chat box

4. Click the down arrow next to "Add"

5. Click "Connect more"

6. Scroll down to Advanced Settings

7. Click the toggle next to Developer Mode (must be "on")

8. Click Back

Step 2: Create MCP Server Connection

1. In the upper right-hand corner, click "Create"

2. Fill in the following:

   • Icon: Optional

   • Name: BV-BRC MCP

   • Description: ''

   • MCP Server URL: https://dev-7.bv-brc.org/mcp

3. Authentication:

   • Leave authentication on OAuth

4. Check the box if you Trust this application

5. Click "Create"

Step 3: Connect to Your Server

1. You should now see 'BV-BRC MCP' under "Enabled apps & connectors"

2. Click the 'X' in the top left to go back to the chat screen

3. In a New Chat, click the '+' button and hover over More

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

4. Select BV-BRC MCP

1. Click account in bottom left and go to settings

2. Click 'Connectors'

3. Click 'Add custom connector'

4. Fill in the following:

   • Name: BV-BRC MCP

   • Remote MCP server URL: https://dev-7.bv-brc.org/mcp

5. Click 'Add'

6. Then click 'Connect'

7. Log into BV-BRC

8. It's now available to use in a new chat

Open your terminal

1. Clone Github Repository

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