MCP server

Brapi

io.github.cyanheads/brapi-mcp-server

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Collaborative BrAPI v2.1 MCP workspace: studies, germplasm, genotypes across Breedbase, T3, more.

Source

At a glance

Type

MCP server

Publisher

Not verified

Status

Working at last check

Tools

22

Token cost

About 14,307 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http brapi-mcp-server https://brapi.caseyjhand.com/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.brapi-mcp-server]
url = "https://brapi.caseyjhand.com/mcp"

Gemini CLI

{"mcpServers":{"brapi-mcp-server":{"httpUrl":"https://brapi.caseyjhand.com/mcp"}}}

Cursor

{"mcpServers":{"brapi-mcp-server":{"url":"https://brapi.caseyjhand.com/mcp"}}}

VS Code

{"servers":{"brapi-mcp-server":{"type":"http","url":"https://brapi.caseyjhand.com/mcp"}}}

Antigravity

agy mcp add brapi-mcp-server https://brapi.caseyjhand.com/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"brapi-mcp-server","server_url":"https://brapi.caseyjhand.com/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"brapi-mcp-server","server_url":"https://brapi.caseyjhand.com/mcp"}

Tools

• brapi_build_phenotype_matrix ~893 tokens
  Pull observations across one or more studies and pivot them into a germplasm × trait matrix materialized as a canvas dataframe. Returns a dataframe handle (read it with brapi_dataframe_describe and brapi_dataframe_query) plus a summary of dimensions and aggregate method. Long-form output is suitable
• brapi_connect ~1125 tokens
  Open a connection to a BrAPI v2 server, authenticate, and return the full orientation envelope (server identity, capability profile, content summary, suggested next tools). Other BrAPI tools connect an alias the server has a URL configured for (a built-in or operator-configured alias, or `default` o
• brapi_dataframe_describe ~246 tokens
  Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`) — pass it as `dataframe` to inspect schema and provenance before writi
• brapi_dataframe_query ~682 tokens
  Run SQL across in-memory dataframes. Dataframes auto-populate when find_* tools spill (named `df_<uuid>`) — the dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`), so the typical flow is find_* → read the name → query here. Use brapi_dataframe_describe
• brapi_describe_filters ~189 tokens
  List the valid filter names for a BrAPI endpoint (studies, germplasm, observations, variables, images, variants, locations) — companion lookup for the `extraFilters` passthrough on any `find_*` tool. Entries reflect the BrAPI v2.1 spec; individual servers may implement subsets.
• brapi_export_genotype_matrix ~770 tokens
  Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `matrix-json` registers a wide canvas dataframe; `vcf-lite` adds VCF-subset text in `vcf`; `plink` adds .ped/.map text in `ped`/`map`. Text formats pull /variants metadata and convert zero-based BrAPI start to one-based
• brapi_find_genotype_calls ~760 tokens
  Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy; when the pull is truncated, narrow the filters. results[] holds the leading calls up to `loadLimit` and a 24,000-byte budg
• brapi_find_germplasm ~947 tokens
  Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with bra
• brapi_find_images ~759 tokens
  Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Returns metadata only — use brapi_get_image to fetch bytes inline. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the match
• brapi_find_locations ~1127 tokens
  Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Countries filter by ISO 3166-1 alpha-3 code via countryCodes, or by free-form English country name via countryNames (resolved client-side to alpha-3 — "Uganda" → "UGA"). Optional bbox parameter restricts
• brapi_find_observations ~918 tokens
  Pull observation records filtered by study, germplasm, variable, season, or observation unit. Without a studies, trials, observationUnits, or observations anchor, a GET query first runs a one-row count probe and skips the bulk pull (warnings says so) when the probe fails or reports more than 5,000 m
• brapi_find_studies ~800 tokens
  Locate studies matching crop, trial type, season, location, or program. Enriches results with program/trial/location context in one call. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a datafram
• brapi_find_variables ~1028 tokens
  Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against every fetched row by PUI, name, synonym, and trait text; a candidate carries the ontology PUI of its row as termId when the row has one. results[] holds the leading rows
• brapi_find_variants ~703 tokens
  Find variant records by variant set, reference sequence, or genomic region (start/end, 0-based inclusive / exclusive per the BrAPI spec; servers may differ). results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materi
• brapi_germplasm_performance ~552 tokens
  Aggregate a single germplasm's observations across studies, returning per-variable statistics (n, mean, median, sd, min, max), contributing studies, seasons, and collection coverage. SGN/Breedbase uses advertised germplasm-scoped observation units with embedded measurements, including zeros. Other s
• brapi_get_germplasm ~264 tokens
  Fetch a single germplasm by DbId with attributes and direct parents. Response companions report study count, direct parent count, and direct descendant count — signals for pedigree depth and observation coverage.
• brapi_get_image ~284 tokens
  Fetch image bytes for up to 5 imageDbIds and return them inline as `type: image` content blocks. Falls back to the metadata `imageURL` when the server lacks dedicated image-content delivery or that request fails. No filesystem side-effects.
• brapi_get_study ~258 tokens
  Fetch a single study by DbId with its program, trial, and location records resolved where those lookups succeed. Response includes cheap observation/observation-unit/variable counts as drill-down signals.
• brapi_raw_get ~534 tokens
  Passthrough to BrAPI GET /{path} without foreign-key resolution. List results (result array or result.data) return a leading preview within loadLimit and a 24,000-byte budget on each serialized row representation; an oversized first row returns no inline rows. Omitted fetched rows remain in a datafr
• brapi_raw_search ~507 tokens
  Passthrough to BrAPI POST /search/{noun}, polling async search IDs. Sends loadLimit as the initial pageSize unless body.page/pageSize drives explicit paging. List previews fit loadLimit and a 24,000-byte budget on each serialized row representation; an oversized first row returns no inline rows. Eve
• brapi_server_info ~278 tokens
  Return the full orientation envelope for a BrAPI connection — server identity, capabilities, content counts, suggested finders, and notes. Pass forceRefresh to refetch the cached capability scan; pass an alias to read a non-default connection.
• brapi_walk_pedigree ~683 tokens
  Walk germplasm ancestry or descendancy as a deduplicated DAG with cycle detection and depth limits. leafCount counts graph terminals, confirmedLeafCount counts successfully verified leaves, and frontier records unresolved directions. Nodes and edges each fit loadLimit and a 24,000-byte preview budge

Browse

• GitHub tools
• Pragma tools
• Hiring and jobs
• GitHub and code hosting
• Databases
• Government and public data

Related MCP servers

• HLA-Verify
  HLA nomenclature and match checks against a pinned IPD-IMGT/HLA release. No patient identifiers.
• Wavetable Tools
  Hyperwave wavetable format lookup, encoder layouts, and float32 mono frame-size calculations.
• Brapi
  brapi.dev MCP — Brazilian stock + crypto + ETF quotes.
• ZeroWidth Prism
  Explore ideas in Prism fields, run studies, and read research findings.
• Jean — Molecular Biology & Genomics
  Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics
• Biostudies
  EBI BioStudies MCP.
• ClinicalTrials.gov MCP by usefulapi
  Search and read ClinicalTrials.gov studies, sites and outcomes.
• Gtex
  GTEx MCP.

Badge for your README

[![AptLynx](https://aptlynx.net/badge/io.github.cyanheads/brapi-mcp-server.svg)](https://aptlynx.net/servers/io.github.cyanheads/brapi-mcp-server)

Listing text is written by the maker; AptLynx lists tools and does not vouch for them. Find another tool · Browse by topic · For agents