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概要と使いどころ
Render a wiki into ONE self-contained HTML snapshot (pages + provenance) that opens offline — no CDN, no remote assets, page content HTML-escaped. Use to share or review accumulated wiki knowledge as a static page. NOT for capturing/approving knowledge (see mk:wiki); NOT for generic code/diagram visuals (see mk:preview).
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CEO/founder-mode plan review. Rethink the problem, find the 10-star product, challenge premises, expand scope when it creates a better product. Four modes: SCOPE EXPANSION (dream big), SELECTIVE EXPANSION (hold scope + cherry-pick expansions), HOLD SCOPE (maximum rigor), SCOPE REDUCTION (strip to essentials). Use when asked to "think bigger", "expand scope", "strategy review", "rethink this", or "is this ambitious enough". Proactively suggest when the user is questioning scope or ambition of a plan, or when the plan feels like it could be thinking bigger. Use AFTER a plan exists. For validating the idea itself before planning, use /mk:office-hours first.
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Design and safely evolve data models, database schemas, migrations, queries, indexes, and ORM data-access boundaries. Use for data-model, migration, query, index, ORM schema, or datastore-selection tasks. Discover the existing engine and migration source before proposing syntax.
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Task-sized forensic analysis of Vivado synthesis and routed timing evidence for processor RTL. Use when Codex must trace a named setup or hold path, audit whole-design timing populations, compare implementation runs, map primitive, LUT, CARRY, BRAM, DSP, MUXF, register, and routed-net stages back to Chisel or generated RTL, distinguish logic from routing pressure, identify missing DCP queries, or write an evidence-backed timing report. This skill is read-only by default and stops at ranked modification directions. Use optimize-chisel-fpga-timing for RTL edits and routed A/B implementation closure.
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Initialize or safely upgrade a processor project's root AGENTS.md from a maintained baseline. Use when starting a processor project, adding project-level Agent collaboration rules, or comparing an existing AGENTS.md with the package baseline. This skill only handles AGENTS.md; it does not scaffold documentation, inspect or configure environments, install tools, or modify processor source.
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Document-driven workflow for implementing, reviewing, and verifying Chisel processor and memory-subsystem RTL. Use when Codex must work from maintained Architecture and Design, trace a complete integration surface, reason in synthesized-hardware terms, keep source-adjacent _codex.md summaries current, avoid redundant or overprotective logic, or run focused functional verification.
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Use when user says "simmer this", "refine this", "hone this", "iterate on this", or asks to improve a specific artifact over multiple rounds. Runs an iterative refinement loop with investigation-first judges that read the code, understand the problem, and propose evidence-based improvements. Auto-selects single judge or multi-judge board based on complexity. Works on any artifact type: documents, prompts, specs, emails, creative writing, API designs, pipelines, codebases. Supports multi-file workspace targets, runnable evaluators, and open-ended optimization (model selection, pipeline topology, prompt tuning).
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Select established CTF and security-research tools for authorized artifact triage, web inspection, reversing, crypto, forensics, networking, and exploit validation. Use when a user provides a CTF-style tool catalog, asks which tools to use, or needs safe usage instructions for common offensive/security tools.
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Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM. Use when subsetting a FASTA/FASTQ file, removing unwanted or low-quality records, or selecting records by specific criteria. Use the paired-end-fastq skill instead whenever the input is paired R1/R2 reads.
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Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA. Covers the direction-not-magnitude principle, local-linear validity, the GRN/velocity error it inherits, baseline discipline (mean and additive baselines), and the validation gap. Use when predicting TF knockout or overexpression effects, ranking driver TFs for fate transitions, or planning perturbation experiments. For GRN construction see multiomics-grn; for experimental Perturb-seq see single-cell/perturb-seq.
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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.
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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.
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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
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Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.
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This skill guides clinicians to inform and counsel individuals seeking gender-affirming medical treatment about fertility preservation options before initiating puberty suppression in adolescents or before starting hormonal therapy in adolescents and adults. It is triggered when a patient is eligible for pubertal suppression or sex hormone treatment and is about to begin such therapy.
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Evaluates patient’s selection of sensor insertion sites and site care to prevent irritation or infection. Triggers include: 'Review CGM site rotation', 'Check sensor site hygiene and adhesion'.
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Guides selection of the optimal confirmatory test (CCT, SIT, FUT, OSLT) for primary aldosteronism based on patient safety and feasibility. Triggers include when a clinician asks “Which confirmatory test should I use?” or evaluates patient comorbidities before testing.
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Suggests genetic counseling for patients with primary adrenal insufficiency (PAI) when a monogenic disorder is suspected. Use when PAI patient presents with early-onset disease, syndromic features, consanguinity, family history, or negative autoimmune antibodies.
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Select the right treatment tier for a child with obesity — behavioural, pharmacologic, or surgical — using the CMAJ 2025 pediatric obesity guideline. Trigger when a clinician asks what to do for a child with obesity, which intervention to start, whether to escalate treatment, or when to consider medication or surgery for pediatric obesity.
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Select the right pharmacologic agent for a child aged 12+ with obesity using the CMAJ 2025 guideline — choosing between GLP-1 receptor agonists, metformin, or orlistat with monitoring guidance. Trigger when a clinician asks which medication to use for pediatric obesity, whether to start semaglutide or metformin in a child, or how to manage obesity pharmacologically in adolescents.
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Guides comorbidity-stratified selection of initial and further glucose-lowering medicines for adults with type 2 diabetes using the NICE NG28 (2026) framework, covering six clinical profiles: no relevant comorbidity, heart failure, atherosclerotic cardiovascular disease, early onset, obesity, chronic kidney disease, and frailty.
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Teaches AI patients about stress-dosing and emergency glucocorticoid administration; instructs to obtain emergency card/bracelet/necklace and kit with injectable high-dose GC. Triggers when counseling any patient with adrenal insufficiency (e.g., "Use when counseling patient with adrenal insufficiency...").
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Run an org-team workflow — a flat pod of up to four peer Claude Code sessions claims lane-tagged slices of an approved spec over the baseline MCP channel and implements them concurrently, each in its own git worktree. Each peer DECIDES its own in-lane implementation choices in its own main context (Article X); only un-decidable or cross-lane forks escalate peer→lead→human (yield_fork for task-bound forks, ask_lead for free-form queries). Opt-in and OFF by default (velocity.org_mode.enabled). Graduates the retired sprint-dispatch prototype into the constitutionally-sanctioned org-team model (Article X — Multi-session coordinated workflows). Requires git.
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