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Clarify priority and emphasis by fixing unclear primary actions, competing visual weight, loud section titles, and weak label/value treatment. Use when the user mentions hierarchy, prioritization, too much competition, grayscale confusion, loud headings, or unclear primary actions.
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Turn product requirements into scoped tasks with dependencies and acceptance criteria. Use for implementation planning and prioritization.
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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.
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Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.
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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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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.
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Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.
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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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Refute-before-prove research discipline: automated counterexample sweeps before any formalization, meter-integrity audits for information-bound experiments, mutation-tested model checkers, pre-registered commit-or-cut gates for speculative directions, wrong-turn reporting, and numeric-claim provenance. Use when validating any new theorem, bound, equilibrium, or security claim; when building or trusting a checker, simulator, or experiment; or when deciding whether a speculative research direction lives or dies. NOT for exploratory brainstorming, product prioritization, writing style, or literature review.
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Discipline an AI agent needs to work an issue/task tracker (Jira, Linear, GitHub Issues) as the shared source of truth: pull the right next item instead of inventing work, search before creating to avoid duplicates, write actionable items with checkable acceptance criteria, keep status transitions honest, and link work to items via branches/PRs/commits so progress is legible. Use when an agent picks up tracker work, files a new issue, updates status, or closes an item. NOT for authoring the PR itself (use agent-pr-authoring), roadmap-level planning and prioritization (use legible-roadmap-with-sidequests), or the mechanics of multiple agents coordinating on the same codebase (use multi-agent-coordination).
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Strategic advisor for Evvo Labs business decisions. Use when Vince asks for strategic advice, business opinions, market entry decisions, pricing strategy, product prioritization, resource allocation, partnership evaluation, competitive positioning, or any question about what Evvo should do next. Applies 5 frameworks: VRIO (competitive advantage), Value Stick (pricing/margin), Blue Ocean (market positioning), McKinsey Horizons (resource allocation), Strategy Diamond (initiative planning). Always read references/evvo-strategy.md before advising.
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Evaluate and prioritize opportunities through a structured filtering process. Use for resource allocation, strategic decision support, and project management.
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Framework-directable information security risk assessment. Identifies threats, evaluates likelihood/impact via a 3x3 matrix, maps findings to any compliance framework, and recommends risk treatment options with prioritization guidance.
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Evaluate strategic options by NPV vs ease of implementation. Use for project prioritization, resource allocation, and strategic decision making.
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Decision validation and thinking frameworks for startup founders. Use when you need to pressure-test a decision, validate your next steps, think through strategic options, or sanity-check your approach. Triggers on phrases like "should I", "help me think through", "is this the right move", "validate my thinking", "what am I missing". Covers fundraising, customer development, runway management, prioritization, and crypto/web3 founder challenges.
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Decide what to build — product strategy, roadmap, feature prioritization, product-market fit, pricing model, backlog, sprint planning, product vision, RICE, JTBD, OKRs. Distinct from designing or building it.
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Code-review quality gate and test-enhancement rubric. Use when ROSE needs sharper review output contracts, severity and risk prioritization, evidence anchors, negative review cases, fixture or golden-output drift guidance, or a Chinese review report profile; do not use as a duplicate code-review agent or final PASS authority.
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Comprehensive OSINT methodology for external red-team operations and authorized attack-surface assessments. Covers the 5-stage recon pipeline (seed discovery, asset expansion, enrichment, exposure analysis, reporting), asset-graph discipline with 29 asset types, severity rubric (CRITICAL/HIGH/MEDIUM/LOW/INFO), confidence upgrade workflows, time budgeting, asset-level triage rules, scale-based tactics, identity-fabric mapping (Entra/Okta/ADFS/Google/SAML/M365 Teams+SharePoint+OAuth), API and auth-map methodology, JavaScript deep analysis, mobile attack surface, cloud attack surface, breach×identity correlation, detectability tagging, detection-aware probing (back-off, persona rotation), read-only validator discipline, WAF/CDN bypass + origin discovery, vulnerability prioritization (CVE/EPSS/KEV), phishing infrastructure planning + pretext development, bug bounty submission templates, client deliverable templates with risk translation, threat-actor investigation (incl. RU/CN pivots), cryptocurrency tracing,...
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Score raw leads as HOT/WARM/COOL based on config-driven weights from agency.config.json
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