"Using Jira MCP API in Python" matching MCP servers:

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

Enables AI agents to resolve scientific names to Taxonomic Serial Numbers, traverse complete taxonomic lineages from kingdom to children, and retrieve vernacular names in all languages from an authoritative US-government taxonomy.

Enables querying gene expression experiments, brain region structure ontologies, and in-situ hybridization datasets from the Allen Institute's Brain Atlas public API.

Exposes the Adaptyv Foundry protein characterization API as MCP tools, enabling AI assistants to interact with experiments, targets, sequences, and results in natural language.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.

Enables AI agents to query Human Phenotype Ontology clinical phenotype terms, navigate term hierarchies, and retrieve gene-disease and disease-phenotype annotations through keyless MCP tools.

Enables automated cell type annotation in scRNA-seq analysis using CellTypist models, with tools for listing, downloading, training, and annotating cell types via natural language.

Enables AI assistants to perform genomic variant analysis using OakVar, including running annotation pipelines, managing 200+ annotator modules, querying variant databases, and generating reports in various formats.

Reproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.

Provides protein family, domain, and functional annotation using InterProScan, supporting local or API backends.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

Enables DNA sequence analysis and variant effect prediction using Evo2-7B via MCP tools, providing forward inference, likelihood scoring, and batch variant comparison through natural language.

Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.

Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.