「modes」の検索結果

Patterns for building entity actors with Akka.Hosting - GenericChildPerEntityParent, message extractors, cluster sharding abstraction, akka-reminders, and ITimeProvider. Supports both local testing and clustered production modes.

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Three modes for CS-conference papers (CVPR/ICCV/ECCV vision, ACL/EMNLP/NAACL NLP, ICLR/NeurIPS/ICML/AAAI ML). DIRECT-EDIT mode (common): the user describes a change in Chinese or English and the manuscript (LaTeX or Markdown) is edited directly through a CS-venue writing toolkit with author sign-off (use for 改这段 / 把中文想法写成 latex / polish / de-AI / translate / compress a passage). REVIEW mode (occasional, pre-submission): harden the paper through an adversarial courtroom review engine (N holistic domain reviewers / contestability routing / two-sided trial / three-way verdict / clerk-converged multi-round loop) with consensus-gated, author-signed revisions (use for review / critique / 审稿 / 评审 / mock-review). AUTO mode (unattended, opt-in via /goal): run the review-revise loop toward a verifiable goal, applying safe fixes under a drift-bounded policy and queueing risky ones. Resolves all inputs at runtime, no hardcoded paths. Not a from-scratch drafter (use ml-paper-writing) and not an official-venue rebuttal.

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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Rank and prioritize neoantigen/epitope candidates by likely T-cell response using NeoFox feature annotation, PRIME2.0, BigMHC-IM, the Łuksza/Balachandran fitness model (agretopicity + foreignness), and pVACtools tiering. Encodes the field's hard truths that immunogenicity is the least-solved layer (dedicated scores ~AUROC 0.6-0.7, modest PPV), that scores are valid only for RANKING within one patient (never absolute go/no-go or cross-patient), that DAI has anchor-inflation and WT-denominator traps, and that stacking weak correlated scores into one number is a red flag. Use when ordering a candidate list for a vaccine. Binding lives in mhc-binding-prediction; calling in neoantigen-prediction.

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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Identifies non-coding RNAs (tRNA, rRNA, snoRNA, snRNA, riboswitches, sRNAs) using Infernal covariance-model search against Rfam, tRNAscan-SE 2.0 for tRNA, barrnap for rRNA, and ARAGORN for tmRNA, plus the small-RNA-seq boundary for miRNA and the transcript-assembly boundary for lncRNA. Covers the structure-conserved-not-sequence-conserved principle (why BLAST fails), GA-threshold and clan-competition correctness, tRNAscan-SE domain modes and pseudogene flags, rDNA copy-number collapse, and why homology annotation is a recall floor. Use when performing genome-wide ncRNA annotation, choosing the right tool for an RNA class, or interpreting ncRNA counts.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Configures and enforces SwiftLint in Swift projects using build tool plugins, run scripts, and CI. Covers .swiftlint.yml configuration, disabled_rules, opt_in_rules, only_rules, analyzer_rules, baselines, autocorrect, swiftlint:disable suppressions, reporter formats (sarif, json, checkstyle), strict and lenient modes, SwiftLintBuildToolPlugin via SimplyDanny/SwiftLintPlugins, swift package plugin swiftlint, Xcode run script phases, CI integration, multiple configuration files, and rollout strategies for existing codebases. Use when setting up SwiftLint, configuring lint rules, suppressing warnings, creating baselines, choosing between build tool plugin and run script, or integrating SwiftLint into CI.

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Writes and migrates Swift Testing framework tests with @Test, @Suite, #expect, #require, confirmation, traits, withKnownIssue, Attachment.record, processExitsWith exit tests and capture lists, Test.cancel, Issue.record warnings/manual failures, XCTest-to-Swift Testing migration, Xcode 27 interoperability modes, XCUITest UI-test boundaries, performance/snapshot boundaries, mocking, async patterns, and test organization. Use when writing tests, converting XCTest assertions such as XCTUnwrap or XCTFail, reviewing advanced Swift Testing API availability, or deciding when to keep XCTest/XCUITest.

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Build direct Bluetooth Low Energy workflows with Core Bluetooth. Use when implementing BLE central or peripheral GATT communication, scanning or connecting with CBCentralManager, discovering services and characteristics, reading/writing/subscribing with CBPeripheral, publishing local services with CBPeripheralManager, handling Bluetooth authorization, background BLE modes, state restoration, write flow control, or CBUUID-based workflows. For privacy-preserving accessory setup/picker flows, use accessorysetupkit first and return here for post-setup GATT communication.

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Transmit and capture RF waveforms using Wireless Testbench with NI USRP radios (X410, X310, N310, N320, N321, N300, X300, E320). Use when generating test signals, transmitting over the air, capturing IQ data, performing loopback tests, configuring multi-antenna setups, or troubleshooting dropped samples and gain settings. Covers basebandTransceiver, basebandTransmitter, basebandReceiver, continuous and once transmit modes, foreground and background capture, and UseRadioBuffer options. Also use when the user mentions transmit waveform, capture signal, IQ data, loopback, RF gain, sample rate, or antenna configuration.

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Discover OPC UA servers, connect MATLAB clients, and browse/navigate server nodes using opcuaserverinfo, the Local Discovery Service (LDS), opcua, connect, setSecurityModel, certificate-trust functions, findNodeById, opcuanode, and Namespace/Children traversal. Use when finding OPC UA servers on the network, querying endpoints and security policies, connecting to a server, authenticating with username/password or certificates, configuring security modes, handling certificate-trust or hostname-mismatch errors, troubleshooting failed connections or empty discovery, inspecting an OPC UA certificate (.der/.pem), browsing an address space, finding nodes by name or NodeId, navigating node hierarchies, invoking method nodes, or batch-processing large namespaces. Trigger on: opcuaserverinfo, LDS, opcua, opc.ua.Client, setSecurityModel, opc.ua.trustServerCertificate, OPC UA certificate, findNodeById, opcuanode, browse OPC UA, find node, OPC UA namespace, OPC UA method node, Industrial Communication Toolbox.

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Verify claims, quotations, citations and references against live primary sources, and produce a reproducible audit record instead of an assertion. Use when asked to: check whether a quotation, verse, statistic, date, attribution or citation is accurate; verify references before publishing a report, thesis, article, slide deck or legal filing; confirm a text against an authoritative database; cross-check a claim across independent sources; build a citation register or verification appendix; find out whether two datasets agree; detect a misattributed or fabricated quotation; or audit a document's existing citations. Source-agnostic by design, with working providers for REST/JSON APIs, scraped HTML, bulk corpora, bibliographic catalogues (OpenLibrary), DOI resolution (Crossref) and reference works (Wikipedia) -- including scriptural tiers (Qur'an.com, sunnah.com and an independent hadith corpus) with full diacritic handling for Arabic, Hebrew, Greek and any script with optional marks. Covers content-addressed matching when sources disagree on numbering, graded match verdicts, byte-level integrity checks, published-string verification, and a catalogue of silent failure modes (identifier divergence, mojibake, scraper blocking, false-positive keyword rules, missing glyphs, unreliable PDF text layers).

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E-commerce product description generator for any platform. Generates optimized titles, bullet points, descriptions, and backend keywords using competitor research + keyword scoring + FABE copywriting. Two modes: (A) Create — generate listing from product specs with optional competitor analysis, (B) Optimize — improve existing listing with keyword gap analysis. Supports Amazon, eBay, Walmart, Shopify, Etsy, TikTok Shop, Lazada, Shopee. No API key required. Use when: (1) writing a new product listing, (2) analyzing what makes competitors rank, (3) improving an underperforming listing.

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E-commerce content marketing strategy planner. Generates content calendars, topic ideas, and platform-specific strategies by analyzing customer reviews, trends, competitor content, and SEO opportunities. Two modes: (A) Build — create a full content strategy from scratch, (B) Audit — analyze existing content and find gaps. Supports TikTok, Instagram, YouTube, Pinterest, blog/SEO, and Amazon A+. No API key required. Use when: (1) planning content for a new product launch, (2) building a content calendar, (3) finding viral content ideas, (4) analyzing competitor content strategies, (5) extracting customer pain points for content topics.

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Cross-platform PPC strategy planner for ecommerce businesses. Analyzes your product and margins, recommends the right advertising platforms (Google Ads, Meta Ads, TikTok Ads), calculates ROAS targets, allocates budget across channels, and generates platform-specific campaign briefs with ad copy and creative direction. Two modes: (A) Build — design a multi-platform ad strategy from scratch, (B) Optimize — audit existing cross-platform campaigns and reallocate budget. Works for Shopify, WooCommerce, standalone stores, and marketplace sellers expanding to external traffic. No API key required.

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Review a business plan or product strategy through the eyes of a smart-money seed/Series-A investor. Asks the brutal questions: Is this fundable? What's the moat? What's the exit story? Outputs a verdict with one of four modes — SEED VIABLE / LATER ROUND ONLY / BOOTSTRAP-ONLY / UNFUNDABLE. Use when the user has a business plan and wants to know if it would survive an investor pitch. Triggered by: 'investor review', 'is this fundable', 'VC perspective', '投资人视角'.

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Review a business plan from the perspective of the named target customer. Asks: would they actually pay this price for this solution today? Outputs a verdict with one of four modes — PAY NOW / PAY WITH FRICTION / WOULDN'T PAY / WRONG ICP. Use when the user has a defined ICP and pricing and wants to stress-test whether the value prop survives contact with reality. Triggered by: 'customer review', 'would they pay', 'pricing reality check', '客户视角', '会付费吗'.

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Plan and execute entire application builds. Generates phased delivery roadmaps, then executes them autonomously — phase by phase, committing at milestones, deploying, testing, and continuing until done or stuck. Modes: plan (generate roadmap), start (begin executing), resume (continue from where you left off), status (show progress). Triggers: 'roadmap', 'start building', 'resume the build', 'keep going', 'build the whole thing', 'execute the roadmap', 'what phase are we on'.

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Audit and improve an entire agentic-development setup, including skills, context, memory, tools, models, permissions, hooks, workflow habits, and secrets hygiene. Invoke for setup reviews, workflow grading, Goblin Mode, or questions about what to improve. Supports shallow, deep, ultra, and yolo modes. Use domain-specific skills for a single model, report, or tenant.

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Stress-test a plan, brief or delivery claim against evidence and plausible failure modes. Use when the user asks for a red team or preparation for a consequential decision.

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