「omics」の検索結果

Run the weak-agent adversarial test harness against docx-cli. Spawns weak exercise agents (Haiku by default, Sonnet to probe, or a local agent harness's pre-produced runs) to perform real document tasks over six scenarios — five editing (MNDA form-fill + font fidelity, invoice table-edit/restructure + logo replace, résumé styling, contract redlining + commenting, contract finalize via accept/reject + comment reply/resolve) and one authoring (T. S. Eliot poetry journal: multi-column, verse, footnotes, links, figure) — renders every result with Word, has opus judge them against ground-truth rubrics, measures each exercise's tool economy, token cost, wall-clock, and correctness (from transcripts for Claude, the exercise.json ledger for the local harness), and synthesizes a prioritized ergonomics report. Use when the user says 'adversarial review', 'test docx-cli with weak agents', 'run the haiku harness', 'weak agent test', or wants to re-run yesterday's adversarial process.

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Think and work like an expert Microbiome Scientist. Use when a task calls for Microbiome Scientist judgment. Reasons from compositional and longitudinal stats (MaAsLin2, ANCOM-BC2), STORMS pre-analytics, FMT/LBP and diet trials, and multi-omics integration; treats PPI/antibiotic confounders, kitome contamination, host-DNA swamping, and HMA causality overclaim as first-class failure modes.

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Think and work like an expert Molecular Neuroscientist. Use when a task calls for Molecular Neuroscientist judgment. Reasons from NPQ transmission, AMPAR/NMDAR trafficking, monoamine receptor/transporter systems, optogenetics (ChR2/Chrimson/ACR) with retinal-artifact controls, AAV/rabies circuit tracing, and region RNA-seq with DESeq2/SynGO—integrating synaptic biochemistry, perturbation, and omics while treating mini-detection bias, TVA leak, and batch/composition confounds as first-class failure modes.

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Think and work like an expert Medical Geneticist. Use when a task calls for Medical Geneticist judgment. Reasons from pedigree priors, HPO phenotype match, and ACMG/ClinGen variant classification; integrates exome/genome, CMA, RNA splicing, NBS ACT pathways, Tier 3 carrier screening, SF v3.3, and CPIC pharmacogenomics while treating VUS overcall, CPM/NIPT discordance, mtDNA heteroplasmy sampling, and SpliceAI-only splicing claims as first-class failure modes.

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Think and work like an expert Microbiologist. Use when a task calls for Microbiologist judgment. Reasons from culturability limits, CFU/MPN enumeration, selective media, DADA2/QIIME2 16S ASVs (SILVA/GTDB), and shotgun metagenomics (Kraken2, MetaPhlAn, HUMAnN); treats plate-count anomaly, compositional stats pitfalls, kit contamination, and index hopping as first-class failure modes.

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Think and work like an expert Glycobiologist. Use when a task calls for Glycobiologist judgment. Reasons from N-/O-glycan biosynthesis, O-GlcNAc cycling (OGT/OGA), LC-MS glycomics, exoglycosidase sequencing, and lectin microarrays; uses GlyTouCan/SNFG/MIRAGE, pGlyco/GlycoWorkbench, and treats PNGase F limits, isomer collapse, and ER-stress high-mannose as first-class failure modes.

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Think and work like an expert Catalysis Engineer. Use when a task calls for Catalysis Engineer judgment. Reasons from catalyst lifecycle margin, space velocity (WHSV/GHSV/LHSV), and deactivation economics through plant historian trends, MAT/pilot trickle-bed activity tests, Aspen HYSYS activity factors, and ASTM crush/attrition plus TPO/ICP spent-catalyst profiling while treating coke, poisoning, sintering, attrition, and channeling/maldistribution as first-class failure modes.

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Think and work like an expert Climate Risk Analyst. Use when a task calls for Climate Risk Analyst judgment. Reasons from TCFD/IFRS S2 four-pillar disclosure, NGFS Phase V orderly/disorderly/hot-house scenarios, hazard–exposure–vulnerability and RMS/AIR/CLIMADA cat economics, transition carbon-price and stranded-asset pathways, and PCAF financed emissions while treating exposure geocoding quality, Kotz damage-function retraction, and scenario-not-forecast misuse as first-class failure modes.

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Think and work like an expert Chemical Biologist. Use when a task calls for Chemical Biologist judgment. Reasons from chemical genetics, ABPP/TPP/CETSA chemoproteomics, and SGC/Portal probe criteria; deconvolves phenotypic hits with PAINS/aggregator triage, inactive analogs, and genetic epistasis while treating colloidal aggregation, probe promiscuity, and degrader DC50/Dmax tag artifacts as first-class failure modes.

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Think and work like an expert Bacteriologist. Use when a task calls for Bacteriologist judgment. Reasons from bacterial growth physiology, selective culture, Gram stain, MALDI-TOF and 16S/WGS identification, EUCAST/CLSI AST, BSL containment, contamination and VBNC, using BacDive and BV-BRC for strain metadata and pathogen genomics.

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Think and work like an expert Bioinformatics Engineer. Use when a task calls for Bioinformatics Engineer judgment. Builds production genomics DAGs in Nextflow/nf-core, Snakemake, and WDL/Cromwell with digest-pinned containers, GIAB regression CI (nf-test, pytest), QC-gated MultiQC runbooks, and CLIA-grade provenance—distinct from analyst-focused bioinformatician DE/GWAS reasoning.

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Think and work like an expert Astrobiologist. Use when a task calls for Astrobiologist judgment. Reasons from habitability, redox disequilibrium, and Bayesian biosignature frameworks through Mars (Perseverance, Viking perchlorate lessons), Europa Clipper ocean worlds, agnostic signatures and the Ladder of Life Detection, while treating abiotic mimics, preservation, and LUCA phylogenomics as constraints—not templates—for extraterrestrial life.

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Produce short-form video with Pika (pika.art) — its effect-driven tools (Pikaffects, Pikadditions, Pikaswaps, Pikaframes, Pikascenes, Pikatwists) and audio-driven lip sync (Pikaformance), plus text-to-video and image-to-video. Use when a task calls for playful, stylized, meme-able social clips, or for applying generative effects and object swaps to real uploaded footage, and when deciding whether Pika is the right engine versus a higher-fidelity model. Covers model versions, credit/plan economics, the fal.ai API route, prompt construction, iteration/repair, capability limits, and consent/rights rules for uploaded real-person media. Not a general "best video model" chooser.

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Produce video (and its supporting stills) through Higgsfield (higgsfield.ai), a multi-model creative platform that fronts third-party video models (Kling, Veo, Seedance, Wan, MiniMax, and, until retirement, Sora) plus Higgsfield's own control layer — Soul / Soul ID image generation, the DoP camera-preset engine, and the Cinema Studio filmmaking suite. Use this skill when a request routes generation through Higgsfield specifically, when the user wants aggregator-level model switching and cinematic camera/effect presets in one workspace, when planning character consistency via Soul ID, or when deciding whether to go through Higgsfield versus direct to an underlying model provider. Covers model selection, per-model prompt strategy, credit economics, the (partial) API surface, capability limits, and rights/consent policy for generated and uploaded real-person footage.

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Provider-independent character design and continuity direction for generated media. Use when an agent must create, preserve, revise, or QA a recurring character across AI-generated images, video clips, avatars, animation, comics, ads, product mascots, serialized social posts, or multi-shot campaigns; especially when building character bibles, reference packs, prompts, expression/pose ranges, costume/hair/makeup/prop continuity, identity and likeness safeguards, iteration plans, handoff notes, or continuity reviews.

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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Processes environmental DNA metabarcoding data from raw amplicon reads to species occurrence tables using OBITools3, DADA2, and taxonomic assignment against BOLD, MIDORI2, or MitoFish databases. Handles COI, 12S, rbcL, and ITS barcode regions with primer removal, denoising, chimera detection, and contamination filtering via decontam. Includes occupancy modeling (occumb) for detection probability correction. Use when analyzing eDNA from water, soil, or bulk samples for biodiversity monitoring. Not for 16S human microbiome (see microbiome/amplicon-processing).

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Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Assesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when estimating effective population size, detecting inbreeding or bottlenecks, or assessing genetic diversity in threatened species from microsatellite or SNP data.

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Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading, saving, or converting single-cell data formats.

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Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.

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Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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