Results for “fish”

Integrate TinyFish web toolkit (search, fetch, browser automation) into Hermes Agent

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Expert-level marine biology covering ocean ecosystems, marine organisms, coral reef ecology, deep sea biology, fisheries science, ocean chemistry, and marine conservation.

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システムログを分析してエラーの根本原因を特定し、段階的に深堀りしていくデバッグ専門家スキル。 アプリケーションログ、システムログ、クラウドサービスログなど様々な形式に対応。 5 Whys、タイムライン分析、Fishbone分析などのRCA（根本原因分析）手法を用いて 問題の本質を突き止め、再発防止策まで提案する。 Use when analyzing system logs to find error root causes, debugging application issues, or performing technical post-mortem analysis with log data. For organizational incident management processes (post-incident review, corrective action plans, incident reports without log data), use incident-rca-specialist instead. Triggers: "analyze this log", "find the root cause", "debug this error", "why is this failing", "log analysis", "what caused this crash", "troubleshoot this issue"

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Tests whether two genomic interval sets overlap (colocalize) more than expected by chance using a permutation test against a structured-genome null model. Covers bedtools fisher (analytic 2x2 screen), bedtools shuffle + jaccard permutation, GAT (isochore/GC-conditioned simulation with FDR), regioneR (flexible permutation, randomizeRegions vs circularRandomizeRegions, localZScore), LOLA (universe-relative Fisher against a region database), and GREAT/rGREAT (regulatory-domain binomial + hypergeometric for ontology-from-regions). Stresses the universe/background choice, matched background, blacklist exclusion, and multiple-testing control. Use when asking whether peaks/regions are enriched at enhancers/TFBS/features, scoring region-set colocalization or region-set enrichment, comparing CNV/SV concordance, or turning an overlap count into a defensible p-value.

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Generates shell completion scripts for CLI tools. Parses command structure from help output, commander/yargs configs, or manual specification. Produces completions for bash, zsh, and fish that follow each shell's conventions.

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Generate jingles, background music, voiceovers, or sound effects with models selected for each audio type. Plan the sound or narration, then save a single MP3 or WAV file in the project folder.

• Create a short jingle for a shop launch
• Generate background music with chosen instruments
• Turn a finished script into narration

Create diagrams that explain systems, workflows, and data relationships using a consistent brand style. The skill guides diagram selection, layout, and readability, with HTML, SVG, and PNG output and support for importing existing diagram formats.

• Explain system architecture
• Visualize workflows and team handoffs
• Restyle existing diagrams to match a brand

Find biological pathways and functions enriched in gene lists or ranked gene data. Choose an appropriate statistical method, align gene identifiers, define comparison backgrounds, and turn results into interpretable tables and plots with multiple-testing corrections.

• Finding enriched pathways among differentially expressed genes
• Running GSEA on a complete ranked gene list
• Calculating gene-set scores for individual samples or cells

Supports medical device quality investigations through CAPA, a process for corrective and preventive action. Helps identify root causes, plan actions, verify results, and report overdue cases, recurrence rates, and other program metrics.

• Investigating recurring quality problems
• Planning corrective actions after audit findings
• Checking whether corrective actions prevented recurrence

Use this skill for BlueField-3 (BF3) day-1 platform bring-up via the classic RShim/BFB path: pushing a BlueField bundle (BFB) to the DPU over RShim with bfb-install from the host, the host-to-DPU TMFIFO management channel (tmfifo_net0, the 192.168.100.x convention), RShim daemon state and console-over-rshim, DPU mode selection (DPU/embedded-function vs separated-host/NIC mode) via mlxconfig, post-BFB recovery, a six-state BlueField-state classifier, and verifying the install (cat /etc/mlnx-release plus version checks). Trigger even when the user does not say "BF3" — typical phrasings include {push a BFB to my BlueField-3}, {bfb-install exited 0 but the DPU never came back}, {ping 192.168.100.2 works but ssh fails}, or {is DOCA on the host or the Arm side?}. BFB reflash, mlxconfig set, mode changes, and firmware burns are destructive: require explicit target-bound confirmation and load doca-hardware-safety. App launch, container deploy, env install, and the BF4 BMC-Redfish path route elsewhere.

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Amazon Aurora PostgreSQL — creates, modifies, and advises on Aurora PostgreSQL clusters specifically (PostgreSQL-compatible engine, Aurora serverless, express configuration, pgvector, Babelfish). Trigger for Aurora PostgreSQL cluster operations, express-configuration quick-start, ACU sizing, I/O-Optimized storage, commitment pricing, or PostgreSQL upgrade planning. For Aurora MySQL, use amazon-aurora-mysql instead. Contains safety guardrails, express-first routing, and response templates that override defaults.

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Systematic Fishbone analysis exploring problem causes across six categories

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终极口播视频 skill：中文口播稿 + 成品配音 → CPU 字级时间戳 → SHOTBOOK 层矩阵分镜 → Remotion 电影感成片（横屏默认/竖屏）。当用户要"做口播视频"、"解说/科普视频"、"把文案变成视频"、"给配音配画面动效"时使用。默认使用成品配音，可选 Fish Audio 从稿子合成配音与时间戳；数字人生成技术不在本 skill 内（人物素材是输入）。含统一视觉语言（Apple 范式）、108 张动效配方卡、镜头三面分层工作单、七层镜头反PPT系统（极缓推拉相机/让位，运动做减法）、六式运动承接转场（每式一卡）、长镜头世界画布、anime.js+three.js 桥、自动静止检测 + 独立 subagent 评估循环。

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Use when asked 写8D报告, 客户投诉8D, 质量问题8D, 客诉回复报告, 8D 怎么写, 根本原因分析报告, or write an 8D problem-solving report for a customer complaint or internal quality issue in a Chinese factory. Produces a bilingual (Chinese and English) 8D report from D0 to D8 with the problem described by 5W2H, dated containment actions and suspect-stock quantities, root cause for both occurrence and escape (流出) with 5 Why and fishbone evidence, verified corrective actions, prevention through updated PFMEA, control plan and SOP, and closure criteria, in the format customers expect.

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Decode an auto repair estimate — what each line actually is, which items are urgent vs upsell, and the questions that separate a fair shop from a fishing expedition. Use when someone asks 'is this repair quote fair', 'decode my mechanic's estimate', 'do I really need all this', or 'is the shop ripping me off'. Produces a line-by-line decode with urgency triage, parts/labor sanity checks, ranked red flags, and the exact questions to ask the shop before authorizing.

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Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

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