F
license-
quality-
maintenanceEnables AI assistants to interact with laboratory devices via a SiLA server, allowing querying device info, listing commands, executing commands, and monitoring status.
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"Executing CLI commands" matching MCP servers:
- AlicenseAqualityAmaintenanceAn MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.29Apache 2.0
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- AlicenseAqualityAmaintenanceMCP server and CLI for detecting, redacting, and auditing PHI in medical text before it reaches AI agents.4MIT
- AlicenseAqualityDmaintenanceEnables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.3169MIT
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- FlicenseAqualityCmaintenanceExposes each stage of the Champollion sulcal embedding pipeline as MCP tools, enabling agents to run, monitor, and debug the pipeline without manual shell commands.17
- AlicenseBqualityBmaintenancePredicts CRISPR gene dependencies and drug targets by integrating literature, regulatory/PPI networks, and genome-scale metabolic models.18Apache 2.0
- AlicenseBqualityAmaintenanceViznoir empowers AI agents to directly analyze and visualize complex 3D scientific and engineering data in cinematic resolution using a fully headless VTK engine. It enables LLMs to seamlessly execute advanced physical analysis, 3D rendering, and generate publication-ready animations purely through natural language commands.2318MIT
Copick MCP Serverofficial
Alicense-qualityCmaintenanceEnables read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.MIT- Alicense-qualityDmaintenanceEnables MCP clients like Claude Desktop to interact with openEHR REST APIs (EHRbase) for creating compositions, managing EHRs, listing templates, and executing AQL queries.18MIT
- Alicense-qualityDmaintenanceEnables Claude to control PyMOL for molecular visualization and structural biology analysis. It uniquely features screenshot capture capabilities that provide a visual feedback loop, allowing the AI to see and verify the results of its commands.MIT
- Alicense-qualityBmaintenanceEnables AI agents to control a local CBCT viewer for dental and maxillofacial scans, with navigation verbs like open scan, set window, navigate slices, and snapshot, without executing code or returning interpretations.3AGPL 3.0
- Alicense-qualityBmaintenanceEnables AI assistants to perform cell segmentation through natural language commands, including 2D/3D segmentation, batch processing, image restoration, and custom model training.BSD 3-Clause
- Flicense-qualityBmaintenanceA terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.
- Flicense-quality-maintenanceAn MCP server for conversational FHIR testing that integrates with the Touchstone platform. It enables users to launch test executions, monitor status, and retrieve detailed results through natural language commands.141
- Flicense-qualityFmaintenanceEnables AI agents to simulate wastewater treatment processes using natural language, with dual MCP and CLI adapters for flexible integration.
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- Flicense-qualityDmaintenanceEnables protein modeling and design using the Rosetta suite via Docker, including structure refinement, mutation stability analysis, docking, and loop modeling through natural language commands.
- -license-quality-maintenanceEnables LLMs to interact with OpenEHR electronic health record systems by retrieving clinical archetypes, generating AQL queries from natural language, and executing queries against on-premise EHR databases. Supports OpenEHR Clinical Knowledge Manager integration and custom IIS-hosted EHR APIs for comprehensive medical data access.