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概要と使いどころ
Designing HTTP cache headers that work correctly across browsers, CDNs, and shared proxies — `Cache-Control` directives per RFC 9111, `stale-while-revalidate` and `stale-if-error` per RFC 5861, the Vary header for varying responses, and surrogate keys for tag-based purging. Grounded in IETF RFCs and Cloudflare/Fastly docs.
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Redis caching patterns, cache-aside, write-through, TTL strategies, and invalidation. Activate on: caching, Redis, cache invalidation, cache-aside, write-through, TTL, CDN cache, stale-while-revalidate. NOT for: CDN/reverse proxy setup (use api-gateway-reverse-proxy-expert), database query optimization (use data-warehouse-optimizer).
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How to design contextual inputs for an always-on AI agent with episodic memory. Covers what data to feed the agent, how to structure observations and triggers, ambient context capture (screen, audio, calendar), context window budgeting, and retrieval strategies that keep the agent grounded in what's actually happening. Activate on: "what should the agent observe", "context inputs for agent", "ambient context capture", "agent triggers", "agent input design", "screenpipe integration", "context window budget", "what data to feed my agent", "/always-on-agent-inputs". NOT for: memory architecture and storage (use always-on-agent-architecture), application ideas (use always-on-agent-applications), safety concerns (use always-on-agent-safety).
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Strategic patterns for solving intractable problems through cascading approximation, self-improvement, and heterogeneous evaluation from DeepMind's AlphaGo system
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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.
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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.
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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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Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essentialome precision-recall AUC against CEGv2 (Hart 2017), Cas9 cut-toxicity diagnostics, copy-number amplicon detection (Aguirre 2016 / Munoz 2016), bottleneck propagation through plasmid pool, infection, selection, and endpoint stages, MOI verification, and DepMap-style screen-quality scoring. Use when assessing screen quality before hit calling, deciding whether to repeat or rescue a screen, diagnosing low-confidence hits, choosing between MAGeCK / BAGEL2 / Chronos based on quality grade, picking a normalization strategy from QC signatures, or evaluating whether an in-vivo screen retained adequate library complexity.
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Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with CVD-safe palettes, cairo_pdf TrueType embedding, programmatic aes via tidy evaluation, and the theme_classic publication baseline. Use when producing static figures in R for papers, presentations, or reports.
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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.
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Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity matrices for clustering, classifying archaea, evaluating MAG (metagenome-assembled genome) species assignment, applying skani for fast metagenomic ANI screening, or reconciling 16S rRNA-based taxonomy with whole-genome ANI.
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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.
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How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.
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Implement semantic vector search with AgentDB for intelligent document retrieval, similarity matching, and context-aware querying. Use when building RAG systems, semantic search engines, or intelligent knowledge bases.
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Interactive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL. Use when searching documentation, managing projects/tasks, or querying indexed knowledge. Provides RAG-powered semantic search, website crawling, document upload, hierarchical project/task management, and document versioning. Always try Archon first for external documentation and knowledge retrieval before using other sources.
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This skill determines whether testicular volume should be used as the primary or sole indicator of sexual development in male childhood cancer survivors who have received gonadotoxic treatments such as alkylating agents or testicular radiotherapy. Triggers include clinician questions like “Can I use testicular volume to assess puberty in this male survivor after chemotherapy?” or “Is testis size reliable for sexual maturity evaluation post‑radiation?”
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Assesses Tanner stage to determine if physical changes of puberty have begun (stage G2/B2 or higher) for considering pubertal suppression. Triggered when a clinician evaluates pubertal development in an adolescent patient.
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Considers adapting the basal insulin rate at hospital admission for patients using insulin pump therapy. Triggered by clinician questions such as "Should we adjust the basal rate upon admission for pump therapy?" or when evaluating pump continuation versus transition to scheduled subcutaneous insulin.
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Assess whether a hospitalized adult with diabetes on insulin pump therapy remains a candidate for continued inpatient pump use. Consider triggers such as the clinician asking "Is this patient appropriate to continue insulin pump in hospital?" and evaluate for impaired consciousness, inability to adjust pump settings, critical illness, DKA, or hyperosmolar hyperglycemic state.
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Evaluates cardiovascular risk factors in persons receiving hormone therapy by obtaining fasting lipid profiles and diabetes screening. Triggered when a patient is on gender-affirming hormone therapy and due for routine cardiovascular risk assessment.
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This skill determines whether an adolescent or adult patient meets DSM-5 criteria for gender dysphoria (gender incongruence) by evaluating the presence of at least two of six specified criteria over a minimum 6-month duration, accompanied by clinically significant distress or impairment. It is triggered when a clinician queries whether the patient's reported symptoms align with gender dysphoria, such as persistent incongruence between experienced/expressed gender and designated gender.
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Determines if an adolescent meets criteria for initiating sex hormone treatment for gender dysphoria/gender incongruence. Triggered when an adolescent requests sex hormones or presents for gender-affirming hormone therapy evaluation.
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Determines whether an adult patient meets eligibility criteria for initiating gender-affirming hormone therapy. Triggered when an adult patient requests gender-affirming hormones or presents for evaluation of hormone therapy eligibility.
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Provides monitoring schedule for transgender females on estrogen therapy, including clinical evaluation, hormone levels, prolactin, electrolytes, BMD, and cancer screening. Triggered when a transgender female is receiving estrogen therapy for gender affirmation.
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