// MCP TOOL REFERENCE

MEDSCI AGENT TOOLS

28 tools from the MedSci Agent MCP Server, categorised by risk level.

// ALL 28 MEDSCI AGENT TOOLS

READ 22 tools

Read parse_fasta Parse a FASTA file and return sequence metadata: IDs, names, descriptions, lengths, and sequence previews. Read acquire_documents Acquire policy-compliant scientific document text from DOI/PMID/PMCID/URL targets with provenance and conte... Read analyze_medical_image Analyze a medical image (X-ray, CT, pathology slide, dermatology photo) using MedGemma Read analyze_molecule Analyze a molecule from its SMILES string. Returns physicochemical properties: molecular weight, LogP, H-bo... Read analyze_sequence Analyze a protein or DNA sequence: compute length, amino acid composition, molecular weight. For DNA, can a... Read fetch_abstract Fetch abstract text and key metadata for a PubMed article by PMID. Returns abstract text, title, MeSH terms... Read lipinski_filter Check if a molecule passes Lipinski Read molecular_similarity Compute Tanimoto similarity between two molecules using Morgan fingerprints (ECFP4). Score ranges 0-1, wher... Read predict_admet Predict ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) properties for a molecule. Return... Read predict_structure Retrieve an AlphaFold-predicted protein structure by UniProt accession. Returns confidence scores (pLDDT), ... Read predict_toxicity Predict compound toxicity Read read_h5ad Read an H5AD (AnnData) file and return metadata: number of observations, variables, column names. Use this ... Read sandbox_fetch_artifact Read a generated artifact or log file from the host-visible workspace path. Enforces path safety checks and... Read sandbox_status Return the high-level state of a Docker sandbox (exists, running, or stopped). Read search_and_analyze Performs deep literature analysis using PaperQA2. Accepts either DOI/PMID paper identifiers (with internal ... Read search_chembl Search the ChEMBL database for bioactive molecules. Find compounds by target, molecule name, or similar str... Read search_clinical_trials Search ClinicalTrials.gov study metadata by condition, intervention, or NCT identifier. Read search_openalex Search OpenAlex for scholarly metadata across disciplines. Returns titles, authors, citation counts, open-a... Read search_pubmed Search PubMed for biomedical literature metadata. Returns titles, authors, journal, publication date, artic... Read search_uniprot Search the UniProt protein database. Find proteins by name, gene, organism, or accession. Returns protein f... Read gene_set_enrichment Perform gene set enrichment analysis on a list of genes. Queries Enrichr or GSEA against MSigDB, GO, KEGG p... Read resolve_identifier_to_sources Resolve a DOI/PMID/PMCID to candidate source URLs with provenance and confidence metadata.

DESTRUCTIVE 1 tools

Destructive sandbox_teardown Stop or remove a Docker sandbox. By default only stops; set remove to true to also delete.

EXECUTE 5 tools

Execute differential_expression Run differential expression analysis between cell groups. Identifies genes that are significantly up- or do... Execute sandbox_run_job Execute a command in an existing Docker sandbox and capture stdout, stderr, exit code, duration, and artifa... Execute cluster_cells Cluster cells in a preprocessed single-cell dataset using Leiden or Louvain community detection. Returns cl... Execute preprocess_omics Preprocess a single-cell RNA-seq dataset: filter cells/genes, normalize, log-transform, and identify highly... Execute sandbox_prepare Create or verify an isolated Docker sandbox for the workspace. Optionally apply a container template and ne...

// FAQ

How many tools does the MedSci Agent MCP server have? +

The MedSci Agent MCP server exposes 28 tools across 3 categories: Read, Destructive, Execute.

How do I enforce policies on MedSci Agent tools? +

Route the MedSci Agent server through the PolicyLayer gateway. Define allow, deny, or approval rules per tool in the dashboard; they are enforced on every call before it reaches the server.

What risk categories do MedSci Agent tools fall into? +

MedSci Agent tools are categorised as Read (22), Destructive (1), Execute (5). Each category has a recommended default policy.

Enforce policy on every MedSci Agent tool call.

Start from MedSci Agent, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

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