「sci」の検索結果

Changing DOCA versions safely: upgrading or downgrading the host DOCA packages, refreshing the BlueField BFB, bumping the NGC DOCA container tag, or rolling back, with the discipline detect -> report -> ASK -> only then a guided upgrade. Trigger on "is there a newer DOCA", "I want the newest DOCA features, can I just apt upgrade in place", "should I move to the next release", "the upgrade stopped midway and dpkg is in a broken state", "my component is being deprecated, what now", or "roll me back", even without the word upgrade. Detect what is installed, find the newer release, report the gap, then STOP and ask for explicit confirmation; never upgrade automatically. Not for a runtime error on an unchanged install (doca-debug). Version detection alone belongs to doca-version, first-time install to doca-setup, any hardware / firmware / reboot step to doca-hardware-safety, and public-docs or sunset routing to doca-public-knowledge-map.

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Use this skill when the user is operating the DOCA Firefly Service container on BlueField — picking the four PTP configuration axes (role / profile / domain / interface), wiring the BlueField PHC + host follower + consumer workload pairing, deciding whether PTP-grade time is even needed (vs. chrony / NTP), or debugging a Firefly deployment where PTP isn't syncing or the host clock isn't following. Trigger even when the user does not explicitly mention "DOCA Firefly" or "PTP" — typical implicit phrasings include "container green but PTP never advances past LISTENING", "Firefly says synced but the host clock still drifts", "sync acquired but offset is tens of microseconds", "my Rivermax SMPTE workload needs PTP", or "is chrony good enough". Refuse and route elsewhere for installing DOCA, host-side chrony / ptp4l config bodies, PTP topology / boundary-clock design, building DOCA apps that read the disciplined PHC, or other DOCA services (DMS, Flow-Inspector, HBN) — those belong to other skills.

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DOCA Rivermax (doca_rmax) receive streams for timing-precise media over IP (SMPTE ST 2110 video / audio, market data, scientific feeds) on a BlueField DPU or ConnectX host, once the Rivermax SDK and its license are installed; getting the SDK or license is doca-setup / doca-public-knowledge-map territory. Trigger on "ST 2110 receive isn't getting frames", "sub-microsecond jitter on my media receiver", "NOT_SUPPORTED from doca_rmax_init", "no recv events after stream start", or "license check failing on a media receiver", even without naming Rivermax. Covers doca_rmax_in_stream sessions, the SDK + license precondition check, doca_rmax_get_*_supported capability queries, pairing with doca-eth queues and doca-flow steering, and DOCA_ERROR_* from Rivermax calls. Refuse and route elsewhere for programming the underlying queue (doca-eth), steering rules (doca-flow), PTP / clock sync (doca-firefly), or best-effort packet I/O.

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Challenge system assumptions against accumulated evidence. Triages observations and tensions, detects patterns, generates proposals. The scientific method applied to knowledge systems. Triggers on "/rethink", "review observations", "challenge assumptions", "what have I learned".

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[omh] Deep dive before a decision: deep research engine - grounding for specs and decisions: study open-source reference implementations with pinned refs, gather live web evidence with citation discipline, verify contested claims, and distill a decision-grounding dossier that planning consumes; for a decision brief use research-brief, for upstream guidance use web-research. Use when the user says: research plan, literature review, research literature, review recent papers, deep research, deep-research, exhaustive research, saturation research.

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[omh] Rust ownership, lifetime, or unsafe trouble: prepare Rust changes with ownership, error, and API discipline, and escalate any unsafe, FFI, or lock-free change to the UB checklist. Use when the user says: rust, rust code, rust skill, rustlang, borrow checker, lifetime error, ownership error, trait bound.

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[omh] Designing an API, server, or data-layer change: prepare server, API, and data-layer contracts — auth boundary, error paths, response shape, and schema/migration discipline — before implementation. Use when the user says: backend, back-end, back end, backend skill, server side, server-side, api design, api contract.

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Generate demo assets (GIF/MP4) from real tmux E2E runs and viewer screenshots using asciinema and Playwright

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Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FASTA) for local analysis, or listing available datasets by species, cell line, or TF name. Don't use to query specific intervals, locations, genes, motif models or expression data.

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Distills a completed user workflow or interaction into a reusable agent skill. Use when the user asks to turn their workflow, interaction, or multi-step process into a skill, or when they say "make this a skill", "create a skill from what we just did", "package this workflow" or similar. Do not use for creating skills from scratch without an existing workflow (use a generic skill-creator for that).

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Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.

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Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.

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Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) search.

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Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.

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Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when you want to query regulatory annotations or raw experimental data across human cell types.

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Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.

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Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

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Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.

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Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

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Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).

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Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

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Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.

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Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search for terms, retrieve details, navigate hierarchies (parents, children, ancestors), look up properties and individuals, get autocomplete suggestions, or access ontology metadata and statistics.

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Constructs deep-links and URLs for the AlphaGenome Atlas website. Supports generating single-variant exploration links (1-based chr:pos:ref>alt), genomic locus views (1-based closed chr:start-end), candidate summary tables, and AlphaGenome reference vs. alternate predictions. Use whenever visualizing, exploring, charting, or linking genetic variants and genomic loci on the AlphaGenome Atlas, or when asked to inspect, view, or link predictions for a genomic variant.

日本語の概要は準備中です。原文の説明を表示しています。