「pathway」の検索結果

Biochemical metabolism of macronutrients and key micronutrients — digestion, absorption, transport, utilization, and excretion — with emphasis on the pathways that matter for dietary-guideline debates (insulin response, lipoprotein metabolism, one-carbon metabolism, iron homeostasis). Use when a question asks what happens biochemically to a food after it is eaten, or when a claim about "metabolic effect" needs to be tested against mechanism.

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Assessing anthropogenic environmental impacts — pollution pathways, habitat destruction and fragmentation, land-use change, invasive species, overharvest, and extinction debt. Covers environmental impact assessment (EIA) methodology, exposure-effect relationships, population viability analysis, IPAT and ecological footprint frameworks, and strategic environmental assessment. Use when quantifying or forecasting human impacts on ecosystems, designing monitoring programs, or evaluating a proposed intervention against a baseline.

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Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

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Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

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Brain-Computer Interface with colored operad security boundaries. Maximally isolated EEG/neural data processing via VM→Container→Process enclosure with GF(3) conservation for Agent-O-Rama neural pathways.

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Comprehensive audit of a user's entire Claude environment — combines Project audit (six-dimension Project Scorecard, seven anti-patterns) with Global audit (six-dimension Global Layer Scorecard) plus Cross-Layer Alignment Check across all nine layers and Evolutionary Recommendations across four pathways. Produces a unified action plan. Use when user says "full audit of everything," "audit my entire Claude setup," "full stack audit," "comprehensive review of my project and preferences," "check everything," or wants the complete health check of both a specific Project AND their global configuration. Also use when a project audit reveals cross-layer issues that require full-stack visibility. Do NOT use for auditing only a Project (use rootnode-project-audit if available) or only global layers (use rootnode-global-audit if available). Do NOT use for single prompt evaluation (use rootnode-prompt-validation if available). Run on Opus 5 or Sonnet 5 at `high` effort (both defaults); depth reduces on legacy models.

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Systematically interpret mass spectra to determine molecular formula, identify fragmentation pathways, and propose molecular structures. Covers ionization method assessment, molecular ion identification, isotope pattern analysis, common fragmentation losses, and purity evaluation.

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Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological relationships across genes and proteins, drugs, diseases, phenotypes, pathways, biological processes, exposures and anatomy. Use this skill to search entities by name, pull direct neighbours and their evidence types, summarise the local network around a disease, and find direct or two-hop drug-disease connections for repurposing hypotheses. Also trigger on PrimeKG, kg.csv, Harvard Dataverse knowledge graph, disease_protein, drug_protein, indication and contraindication edges, or network pharmacology over a biomedical knowledge graph.

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Curate, review, or repair ai-gene-review ModuleReview YAML documents under modules/, including pathway/module boundary setting, parts and variant modeling, annoton-level molecular functions, representative UniProt/PTN grounding, module deep-research provenance, validation, rendering, and project batch updates.

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Research and populate tracked stablecoin compliance sidecars for the U.S. GENIUS Act, EU MiCA, or both. Use when adding or auditing authorization, applicability, pathway, or disclosure evidence.

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Use when a task needs the judgment of a Biofuels/Biodiesel Technology and Product Development Manager — deciding whether a lab/bench-scale process is ready to scale up, evaluating feedstock flexibility tradeoffs in process design, pricing a technology's value against regulatory credit pathways (RFS RIN, LCFS CI score), or managing IP strategy for a novel conversion process. Distinct from biofuels-production-manager, which runs an existing operating facility — this role owns R&D and commercialization of new or improved process technology.

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Analyze learning management and training pathway systems for prerequisite mapping, competency-based progression, adaptive sequencing, and credential stacking.

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Analyze mental health care planning systems for treatment goal alignment, intervention scheduling, progress milestone tracking, multi-provider coordination, step-down/step-up criteria, and individualized care pathway optimization..

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Drafts FDA 510(k) Premarket Notification submissions demonstrating substantial equivalence under 21 CFR Part 807. Supports Traditional, Special, and Abbreviated pathways. Use when preparing Class II medical device regulatory filings, substantial equivalence analyses, or FDA premarket submissions.

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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.

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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Nat Commun 12:1302), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Expert-level medical device design covering regulatory pathways, design controls, biocompatibility, sterilization, risk management, and verification and validation.

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Use when mapping funnel-stage to content shape — conversion-pathway, content-as-system, leverage-point selection. Triggers on 'design our content funnel', 'why does mid-funnel leak'.

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Knowledge base from the DoD Risk, Issue, and Opportunity (RIO) Management Guide for Defense Acquisition Programs (OUSD R&E, Sep 2023 incl. Change 2.2). Use for the defense-acquisition mechanics of program risk management: the RIO definitions (risk/issue/opportunity), the five-step risk process (plan-identify-analyze-mitigate-monitor), 1-5 likelihood/consequence scoring and the 5x5 risk matrix, the four mitigation options (accept/avoid/transfer/control), burn-down plans, issue management (probability=1), opportunity management toward should-cost, cross-program/interface risk, tailoring RIO to the six AAF acquisition pathways (UCA/MTA/MCA/Software/DBS/Services), specialized methods (RMF, MBCRA/Cyber Table Top, Agile metrics, FMECA, ITRA/DTRAM), and institutionalizing RIO via the PRMP, boards (RMB/JRMB/ROMB/RWG), tools, tiered roles, and WBS/IMP/IMS/EVM/TPM integration. This is the DoD-acquisition complement to nasa-risk (general CRM/RIDM theory) and dau-se-guidebook (the SE process frame). Does NOT teach general risk theory from scratch, and defers specialized risk regimes (system safety/ESOH, HSI, detailed cyber/RMF, spectrum) to their own DoD instructions and the relevant packs.

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Knowledge base from the DoD Test & Evaluation Enterprise Guidebook (August 2022 edition 8.02) with DOT&E-facing enterprise emphasis. Use for T&E enterprise roles (DOT&E vs USD(R&E)), DT&E/OT&E/LFT&E, cybersecurity T&E, MOSA/automation/digital enablers, suitability/reliability growth, and TEMP/Strategy/STE planning. Distinct routing from dod-te-guidebook (same guidebook family, pathway-deep pack). Guidance only—defer to DoDI 5000.89 and Title 10 for binding requirements.

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Knowledge base from the OUSD(R&E) guidebook Implementing a MOSA in DoD Programs (Feb 2025). Use for the Modular Open Systems Approach as a DoD acquisition + design discipline: the statutory/regulatory basis (10 U.S.C. 4401–4403, FY2017/FY2021 NDAA, DFARS), the five OUSD(R&E) pillars, the plan→modularize→identify→define→standardize interface lifecycle, technical levers (WBS/MIL-STD-881F taxonomy, standards profiling, API-first software, COTS/cybersecurity), MOSA assessment metrics and tools (PART/OAAT/KOSS/SEAM/MAUT), technology-change and DMSMS management, roadmaps, MOSA across the six AAF pathways, and contracting/IP/data-rights mechanics. SCOPE LIMITS: this is U.S. DoD weapon-system acquisition policy, not a general open-architecture or interface-standards reference — it names standards (FACE, OMS, DISR) without reproducing them, is light on detailed engineering of any specific standard, and does not cover the underlying SE processes (use dau-se-guidebook / nasa-npr-7123) or general systems-engineering theory (use sebok).

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Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

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