"Java command reference and usage" matching MCP servers:

MyChart MCP Server

An MCP server and TypeScript client SDK that gives AI assistants access to OOREP's homeopathic repertory and materia medica reference data, enabling natural language searches for symptoms, remedies, rubrics, and repertorization across 12+ repertories and 600+ remedies.

Russian drug reference for AI agents: check ГРЛС registration, get a drug card, look up ЖНВЛП price caps, check recalls, and link the official instruction straight from the state registers.

A reference MCP server for clinic scheduling and intake, demonstrating production patterns like tenant isolation, idempotent writes, and structured errors using synthetic data.

Provides fast lexical and optional semantic search over NiiVue neuroimaging visualization library documentation and API reference. Enables LLMs to query guides, retrieve API documentation from TypeScript source, and access structured information through cached BM25 and embedding-based search.

Enables medication reference workflows including drug search, dosing calculations, Taiwan regulatory lookups, hospital prescription helpers, and educational PK/DDI simulation.

MCP server for controlling UCSF ChimeraX molecular visualization software, enabling command execution, screenshots, structure analysis reports, and session management.

MCP server for connecting Claude Desktop to FHIRfly healthcare reference data APIs, enabling lookup of drugs, providers, clinical codes, and more.

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

Provides access to Allen Institute for Neural Dynamics (AIND) metadata and data assets through MongoDB queries, aggregation pipelines, NWB file exploration, and AI-powered data summaries.

Bridge any AI coding assistant directly to GenePattern — run bioinformatics modules, manage cloud jobs, and stream results, all through natural language.

A Model Context Protocol (MCP) server that enables AI agent access to Synapse entities such as Datasets, Projects, Folders, Files, Tables, and more.

Enables AI assistants to look up, search, validate, navigate hierarchies, and expand value sets for SNOMED CT clinical terminology through the Model Context Protocol.

MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.

Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.

Enables MCP clients like Claude Desktop to interact with openEHR REST APIs (EHRbase) for creating compositions, managing EHRs, listing templates, and executing AQL queries.

Provides access to BioThings.io APIs for comprehensive gene and variant annotations, enabling seamless integration of biological data into workflows.

Enables AI assistants to perform DNA/RNA sequence alignment using BWA (Burrows-Wheeler Aligner), supporting both short and long read alignment to reference genomes with indexing, BWA-MEM, and BWA-backtrack algorithms.

An MCP server that provides SNOMED CT clinical terminology lookup via any FHIR R4 terminology server supporting SNOMED CT and ECL. Offers tools for searching by term, fetching by code, and navigating the concept hierarchy.

Enables AI agents to query the PomBase fission yeast model-organism database for genetic and molecular data through the Pipeworx MCP gateway.