Biomedical Research MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| BIOMED_LOG_LEVEL | No | Logging level | INFO |
| BIOMED_RESEARCH_TOP_K | No | Number of evidence results | 5 |
| BIOMED_MCP_SERVER_SCRIPT | No | MCP server script | server.py |
| BIOMED_MCP_SERVER_COMMAND | No | MCP server command | python |
| BIOMED_DEFAULT_DOCUMENT_ID | No | Default research document | DOC001 |
| BIOMED_MAX_QUESTION_LENGTH | No | Maximum agent question length | 2000 |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| calculate_dilutionC | Calculate dilution using C1V1 = C2V2. |
| get_experimentB | Retrieve one experiment by experiment ID. |
| search_experimentsC | Search experiments using:
|
| add_experimentC | Add a new experiment to the database. |
| get_research_documentB | Retrieve research document metadata. |
| add_research_documentC | Add research document metadata. |
| extract_pdf_textB | Extract text from a PDF and save it into research_content and research_pages. |
| get_research_contentC | Retrieve extracted research document content. |
| search_research_contentC | Search extracted research pages using SQL text matching. |
| search_research_evidenceC | Retrieve relevant biomedical evidence using the local retrieval system. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| experiments_resource | Return all experiments as a resource. |
| documents_resource | Return all research documents. |
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