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Mgnify

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MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they…

v0.1.1 · active · repository · website · descriptor JSON · versions

An agent can connect right now, no human step.Remote endpoint, no authentication, reachable on the last probe.
Quality–not scored
Trust97of 100
Uptime, 30 days98%
Latency p5027 ms

Connect

8 clients · secrets stay placeholders
{
  "mcpServers": {
    "mgnify": {
      "type": "http",
      "url": "https://gateway.pipeworx.io/mgnify/mcp"
    }
  }
}
claude mcp add --transport http mgnify https://gateway.pipeworx.io/mgnify/mcp
[mcp_servers.mgnify]
url = "https://gateway.pipeworx.io/mgnify/mcp"
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "mgnify": {
      "type": "remote",
      "url": "https://gateway.pipeworx.io/mgnify/mcp",
      "enabled": true
    }
  }
}
{
  "mcpServers": {
    "mgnify": {
      "type": "http",
      "url": "https://gateway.pipeworx.io/mgnify/mcp"
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=mgnify&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vZ2F0ZXdheS5waXBld29yeC5pby9tZ25pZnkvbWNwIn0%3D"
}
{
  "servers": {
    "mgnify": {
      "type": "http",
      "url": "https://gateway.pipeworx.io/mgnify/mcp"
    }
  }
}
{
  "mcpServers": {
    "mgnify": {
      "httpUrl": "https://gateway.pipeworx.io/mgnify/mcp"
    }
  }
}
extensions:
  "mgnify":
    enabled: true
    name: "mgnify"
    type: streamable_http
    uri: "https://gateway.pipeworx.io/mgnify/mcp"
    timeout: 300

Quality – / 100not scored

Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.

protocol75 · weight 25
  • warn
    protocol.modernnewest supported version is 2025-03-26; 2026-07-28 not supported, older versions are deprecated until 2027-07-28
  • n/a
    protocol.statelessonly applies to 2026-07-28 servers
  • pass
    protocol.transportstreamable HTTP
  • n/a
    protocol.list_ttlonly applies to 2026-07-28 servers
authorizationn/a · weight 15
  • n/a
    auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
  • n/a
    auth.secret_in_urlno templated URL
tool hygienen/a · weight 30
  • n/a
    tools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)
stabilityn/a · weight 15
  • n/a
    stability.changes, stability.rug_pulltool list unknown
dependenciesn/a · weight 15
  • n/a
    deps.known_vulns, deps.mcp_sdk_version, deps.resolvableno npm or PyPI package

Tool list unknown · tools last changed 2026-10-09 · checked 2026-10-20 12:13 UTC

Tool changes

  • subscriberemoved

    Create a proactive monitoring subscription to a live-data event stream. Returns the new subscription id. Requires a Pipeworx OAuth account (anonymous + BYO cannot persist subscriptions). Supported types: "sec_8k" (8-K filings matching ticker + item codes — e.g. items:["5.02"] = officer change), "polymarket_edge" (Polymarket↔Kalshi cross-venue mispricings — params:{topic:"fed"}), "fred_series" (new FRED observations — params:{series_id:"UNRATE"}), "patent_grant" (new USPTO grants for an applicant), "clinical_trial" (new/updated ClinicalTrials.gov studies), "form_d" (new SEC Form D fundraise notices — params:{state?, industry?, min_amount?, exemption?}, all optional), "news_keyword" (GDELT keyword news alerts, metadata+link only — params:{query, lang?, domains?}), "job_post" (new public job-board postings — params:{ats?, board_token?} or {domain?}, plus optional title_query/location_query), "tool_diff" (re-runs any read-only tool on a schedule and fires on change — params:{tool, args?, fields[], schedule}). Delivery channels: feed (always on — pull via recent_alerts or GET registry.pipeworx.io/alerts.json), and optionally email (set delivery:{email:"[email protected]"}) or sms (delivery:{sms:"+15551234567"} — phone must be verified at /account first; 10/day cap).

  • polymarket_fill_riskremoved

    Realizable-vs-theoretical edge check against live CLOB order-book depth. REQUIRES one of `market` (single-market mode) or `event` (basket/partition mode). SINGLE-MARKET: pass a market slug/URL + side (buy_yes|sell_yes|buy_no|sell_no, default buy_yes) + size_usd (default 1000 — max spend on buys, target proceeds on sells); walks the ladder and returns top_of_book, vwap_fill_price, slippage_pp, shares_filled, max_fillable_usd, and a verdict (clean|degraded|cannot_fill). BASKET: pass an event slug/URL + side (sell_yes = capture overround by selling every leg, buy_yes = capture underround; default auto from partition sum) + size_usd interpreted as settlement notional S (shares per leg; each share pays $1); returns theoretical_sum vs realizable_sum (top-of-book vs VWAP across all legs), capture_ratio, profit_usd at executed size, per-leg fill detail, thin_legs[], max_clean_notional_usd, and forced_directional_risk naming the legs most likely to strand you unhedged. USE THIS before acting on any polymarket_arbitrage SELL/BUY-EVERY-LEG signal or any polymarket_edges trade above ~$500 — theoretical overround on thin books is not capturable, and partial basket fills convert an arb into an unhedged directional position (the dominant loss mode in real arb-bot P&L). FEES ARE NOT MODELLED HERE: vwap_fill_price/profit_usd are GROSS of Polymarket's own taker fee (rate 0.04-0.07 by category — see polymarket_edges/fees.ts), on top of which this tool prices depth-crossing cost; a thin-margin fill that looks clean here can still be net-negative after the fee.

  • polymarket_edgesremoved

    Scan top Polymarket markets and return opportunities where Pipeworx data disagrees with market price. Built for "what should I bet on today" — agents discover opportunities without paging hundreds of markets. FIVE MODEL FAMILIES grouped into three response segments under by_segment: (1) MODEL_DRIVEN — crypto_price (lognormal barrier from 90d FRED log-returns) and news_momentum (GDELT 7d/21d article-volume ratio, soft signal w/ halved Kelly). (2) STRUCTURAL_ARBITRAGE — partition_overround on mutually-exclusive events; per-leg favorite-longshot bias correction with per-sport α (tennis 1.02, soccer 1.10, MMA 1.15, default 1.0); placeholder-slug filter drops will-person-X / will-team-Y / will-manager-Z / will-someone-else- backstops; partitions with >20% placeholder fraction skipped entirely. (3) CONCENTRATED_LONGSHOT — basket trade when one leg ≥75% AND ≥2 longshots ≤8% AND portfolio return ≥25:1; rare-by-design (gates relaxed Run 8 from prior 85%/5%/50:1). EVERY OPPORTUNITY carries edge_pp_net (net of slippage AND Polymarket's own taker fee — fees_pp_applied itemises the fee component; see fees.ts for the published per-category schedule), kelly_fraction + kelly_fraction_half (capped at 0.25), market.liquidity, market.spread_pp, market.volume, plus a 24h-move warning ("Market moved X.Xpp in 24h") when the recent move alone exceeds the edge — your edge may already be in the price. TRADEABLE-EDGE KNOBS: min_liquidity / max_spread_pp drop opportunities where edge isn't realizable; min_partition_leg_kelly filters partitions by best per-leg Kelly. RESPONSE TOP-LEVEL: by_segment{model_driven,structural_arbitrage,concentrated_longshot}, fed_candidates/fed_note (Fed bets surface here, excluded from ranking — 1m-T vs EFFR signal is unreliable at meeting-month horizons without paid OIS/SOFR-futures data), and _diagnostics{concentrated_longshot:{...funnel counters},category_counts,filter_skips} so callers can see WHY a segment is empty (top-N stale, all candidates failed gates, knob dropped them). Cached 1h at the KV level keyed on all knobs.

  • company_factsremoved

    TYPED, DETERMINISTIC financial facts for a US public company for an EXPLICITLY NAMED reporting period — "Apple revenue for fiscal 2023", "Walmart net income FY2026 Q3", "Microsoft cash at the end of fiscal 2024". PREFER OVER entity_profile / get_company_financials whenever the period matters: those answer "the most recent figures" and will happily hand back FY2025 when you asked about FY2019, and neither separates a discrete quarter from a year-to-date figure. This one refuses instead — it NEVER substitutes the latest period for the period requested, NEVER returns 0 for missing data, NEVER lets a 9-month YTD number answer a quarterly question, and NEVER converts a currency. Every answer carries the exact us-gaap concept it came from, what that concept MEASURES (NetIncomeLoss excludes non-controlling interests, ProfitLoss includes them — not synonyms), the accession number and a link to the filing on sec.gov, the restatement trail of any superseded figures, and a contract + derivation version to pin against. Fiscal periods are the FILER'S OWN, anchored on their fiscal-year end, so Walmart's year ending 2026-01-31 is FY2026 and Apple's ending 2025-09-27 is FY2025. Attributes in v1: revenue, net_income, cash. Every non-answer is a named status — `unavailable` (the filer did not report it for that period; the periods that DO exist are listed, without values), `unsupported` (outside what v1 covers — a non-us-gaap filer, an unknown attribute, a non-USD unit), `ambiguous` (the company name matched two filers equally well; both are named), `conflicting` (two filings the same day disagree; both are returned and neither is picked), `partial` (a value with no accession behind it). Source: SEC EDGAR XBRL companyconcept, one publisher read once — see `corroboration`. Same response is served at POST https://gateway.pipeworx.io/v1/facts for non-MCP callers.

  • mgnify_genomesremoved

    Search MGnify's species-level genome catalogues — ~57,000 metagenome-assembled genomes (MAGs) and isolates from human gut, soil, marine, chicken and other biomes. AUTHORITATIVE for "is there a genome for this uncultured taxon" and for MAG quality questions: every hit carries GTDB taxon lineage, CheckM completeness and contamination, N50, contig count, GC content, geographic origin, and cross-references to ENA/NCBI accessions. PREFER OVER WEB SEARCH for microbial genome-catalogue lookups. Free-text search runs upstream; catalogue_id and taxon_lineage are applied here over the fetched pages because the upstream silently ignores them.

  • polymarket_arbitrageremoved

    Find arbitrage opportunities on Polymarket via monotonicity violations + partition-sum checks. Call with NO args for a `trending_scan` of the top ~200 markets by weekly volume; pass `event` for the strongest per-event partition_check, or `topic` for a themed cross-event scan. `event` (recommended for a specific market): pass a Polymarket event slug like "fed-decision-may-2026" or "when-will-bitcoin-hit-150k"; walks child markets, checks date-axis / threshold-axis ordering AND computes the partition_check (sum of YES prices across mutually-exclusive legs — should ≈1; deviations >3pp emit a BUY/SELL EVERY LEG signal). `topic` (for cross-event scanning): pass a seed question like "Strait of Hormuz traffic returns to normal" or "Fed rate decision"; searches related events across the platform, flattens markets, runs the comparator on the union. Cross-event mode catches "...by May 31" vs "...by Jun 30" patterns that single-event misses. SEMANTIC ANCHOR: cross-event pairs require ≥0.30 Jaccard similarity on question tokens (prevents Powell-Fed-Pause being paired with Powell-DOJ-probe); skipped_low_similarity surfaces the rejected pair count. PARTITION FILTER: drops will-person-X / will-manager-Y / will-someone-else- placeholder slugs; partitions with >20% placeholder fraction return null arb signal. Response: opportunities[] (gap_pp, suggested_trade, reasoning, monotonicity violation context), and in event mode partition_check{sum_yes_prices, gap_from_1, placeholders_filtered, suggested_trade}. FEES: every opportunities[] row and partition_check.arbitrage carry edge_pp_gross (== gap_pp / overround_pp), fees_pp, edge_pp_net, net_positive, plus polymarket_fee_pp, fee_basis and fee_categories[]. BOTH cost components are modeled: Polymarket's own per-category TAKER FEE (fee = shares × rate × p × (1-p), rates crypto 0.07 / sports-economics-culture-weather-other 0.05 / finance-politics-mentions-tech 0.04, geopolitics and world events fee-free; verified against Polymarket's own docs as of 2026-09-13) and Polygon gas (~$0.02/leg). The taker fee dominates: ~$1.75 per 100 shares on a crypto market at 50c versus $0.02 of gas, so rows that looked profitable before fleet #1927 may now show net_positive:false — that is the correction, not a regression. Each leg is priced at ITS OWN market's rate and price (the fee curve peaks at 50c and falls toward both extremes). fee_basis says where the rate came from: 'payload' (read off the market, the normal case), 'category' (mapped from its fee category), 'fee_free', or 'fallback' (rate unknown — charged at the modal 0.05 rather than assumed free, so an unreadable market is never reported as costless). Where fill_check reprices against live depth, this does NOT double-count that spread cost. FILL CHECK: when the partition signal fires, arbitrage.fill_check prices it against live CLOB depth (theoretical_edge_pp_at_book vs realizable_edge_pp at 1000 shares/leg, thin_legs[]) — realizable_edge_pp ≤ 0 means the overround exists only at last-trade, not in the book; do not trade it. For custom sizing use polymarket_fill_risk.

  • unsubscriberemoved

    Cancel a subscription by id. Ownership is enforced — you can only cancel your own subscriptions. The row is deactivated (not deleted) so its historical events stay available via recent_alerts.

  • mgnify_studyremoved

    Fetch one MGnify metagenomics study in full by its accession (MGYS…) — title, controlled biome classification, the ENA project and study accessions behind it, available downloads and last-update date. Use after mgnify_search_studies, or when a paper cites an MGYS accession and you need to know what it actually is.

  • resolution_auditremoved

    Extract the settlement clause of a single Polymarket or Kalshi market: who publishes the settling number (source), the clock time + timezone it is taken at, the precision of the computation (e.g. "1-minute candle close" vs "60-second trailing average" vs "election outcome"), the evidence standard (official_source | consensus_reporting | any_credible_report | unspecified), and void_handling (cancellation/postponement settlement — reused verbatim from bet_research's cancellation_rule detector, not re-derived). Parses Polymarket's `description` field (fetched via polymarket_market) or Kalshi's `rules_primary` + `rules_secondary` fields (fetched via kalshi_market) with regex + a small vocabulary — no LLM pass, so an unusual clause reports confidence:"low" rather than a guess. Pass `market` as a Polymarket slug/URL or a Kalshi market ticker (e.g. "KXBTCD-26SEP1317-T66999.99"); a Kalshi EVENT ticker (e.g. "KXBTCD-26SEP1317") also works — it picks one representative market under that event, since the settlement mechanism is normally shared across all strikes/legs in one event. Use this before treating a polymarket_kalshi_spread row as a real arbitrage: two ladders that look alike can settle on different sources, at different times, with different precision — this tool is how you check. Pair with resolution_diff to compare two markets directly. KNOWN GAP: idiosyncratic phrasing that doesn't match the vocabulary returns confidence:"low" and evidence_standard:"unspecified" rather than an LLM-guessed answer.

  • polymarket_kalshi_spreadremoved

    Cross-venue spread between Kalshi and Polymarket for the same resolving question. The two venues sometimes price the same outcome 2-25pp apart because their participant pools differ — when the bet shapes are equivalent that delta is a real signal, when they aren't the tool says so. TWO MODES: (1) `topic` — 11 pre-mapped macro subjects ("fed", "btc", "eth", "cpi", "gdp", "sp500", "recession", "next_pope", "next_uk_pm", "next_israel_pm", "2028_president") auto-fetch the matching event on each venue. You do NOT have to use those exact keys: the topic is resolved through aliases and keywords, so "bitcoin", "fed rate decision", "inflation", "s&p 500" and "next pope" all land on the right subject, and `resolution.topic_matched_by` tells you whether it was an exact key, a known alias, a phrase found inside a longer question, or a single-keyword guess — treat "phrase" and "token" as a GUESS at what you meant. An unresolvable topic returns error:"mapping_failed" with mapping_stage:"topic_unrecognized" and known_topics[]; it never silently falls back to a default subject. (2) explicit `kalshi_event_ticker` + `polymarket_event_slug` for custom pairings — BOTH modes run the identical token-overlap matcher, so the same disclosures apply to both. `resolution` is returned in BOTH modes and says how each side's identifier was picked (which Kalshi series was queried, how many events came back, whether the chosen one had quoted markets; which Polymarket search query ran and why that event won). Fleet #2064: when two Polymarket candidates tie on resolution time `polymarket_selected_by` now SAYS so, names every tied slug, names the tie-break that actually decided it (the candidate whose metric_type matches the Kalshi series, else lexicographic slug order), and states whether the winner's metric matches the Kalshi series — it used to assert "picked the soonest-resolving" byte-identically on calls that returned DIFFERENT events, because the tie was settled by upstream fetch arrival order. RESPONSE: each venue's leg-by-leg prices (raw probability 0-1) plus matched spread[].top_spreads_pp (Kalshi − Polymarket) where the same outcome shows up on both sides. SAFETY FIELDS: compatibility_warning is a sentence and compatibility_codes[] the machine-readable form; BOTH can be non-empty on returned pairs, so read them even when matched_pairs>0. Codes: event_subject_mismatch (the two event titles share no subject words — probably not the same question), temporal_mismatch (the two events are about different SUBJECT months — e.g. Kalshi "CPI in October" vs Polymarket "September Inflation"), temporal_alignment_unknown (the subject month could not be parsed on one or both sides — NOT the same as confirmed-aligned; check each event yourself), non_equivalent_bet_shapes, no_candidate_pairs, unclassified_legs_excluded, pairing_unverified (set in EITHER mode whenever pairs are returned: the legs were matched by keyword and word overlap, not a shared resolution source). Each entry in top_spreads_pp carries its own flags[] (temporal_mismatch, temporal_alignment_unknown, event_subject_mismatch, low_token_overlap). A leg whose metric_type or match_subtype is "unknown" is NEVER paired — those comparisons land in spread.skipped_unclassified and, when the wording lined up, in spread.low_confidence_pairs[] for inspection only. temporal_alignment{polymarket_month,kalshi_month,aligned} tells you whether the two events are about the same SUBJECT calendar period, in EITHER mode — this is the period the question is ABOUT (e.g. "September" for a CPI release that settles in October), not necessarily when either side settles; null means it could not be computed (see temporal_alignment_unknown), not that the two sides align. Fleet #2062: this used to compare Polymarket's settlement date against Kalshi's subject month and call a match — fixed to compare subject month to subject month on both sides. FEES: every top_spreads_pp and low_confidence_pairs[] row carries edge_pp_gross (== |sp

Showing the latest 10. Full history: list_changes · trend: quality JSON.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 97 / 100

provenance90
liveness99
freshness100
hygiene100

+repository +namespace-matches-repo +website +reachable +uptime-98% +updated-24d-ago

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Endpoints

remoteauthreachableuptime 30dp50protocollast ok
https://gateway.pipeworx.io/mgnify/mcp streamable-httpnoneyes98%27 ms2025-03-262026-10-20

Tools (0)

No tools observed. Tools appear once a credential-free probe can list them.

Schemas: list_tools.

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Official server.json
{
  "name": "io.github.pipeworx-io/mgnify",
  "title": "Mgnify",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "remotes": [
    {
      "url": "https://gateway.pipeworx.io/mgnify/mcp",
      "type": "streamable-http"
    }
  ],
  "version": "0.1.1",
  "repository": {
    "url": "https://github.com/pipeworx-io/mcp-mgnify",
    "source": "github"
  },
  "websiteUrl": "https://pipeworx.io/packs/mgnify",
  "description": "MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they…"
}