AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Shared vocabulary for designing deep modules. Use when the user wants to design or improve a module's interface, find deepening opportunities, decide where a seam goes, make code more testable or AI-navigable, or when another skill needs the deep-module vocabulary.
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Design deep modules: a lot of behaviour behind a small interface, placed at a clean seam, testable through that interface. Use this language and these principles wherever code is being designed or restructured. The aim is leverage for callers, locality for maintainers, and testability for everyone.
Use these terms exactly: don't substitute "component," "service," "API," or "boundary." Consistent language is the whole point.
Module: anything with an interface and an implementation. Deliberately scale-agnostic: a function, class, package, or tier-spanning slice. Avoid: unit, component, service.
Interface: everything a caller must know to use the module correctly: the type signature, but also invariants, ordering constraints, error modes, required configuration, and performance characteristics. Avoid: API, signature (too narrow, they refer only to the type-level surface).
Implementation: what's inside a module, its body of code. Distinct from Adapter: a thing can be a small adapter with a large implementation (a Postgres repo) or a large adapter with a small implementation (an in-memory fake). Reach for "adapter" when the seam is the topic; "implementation" otherwise.
Depth: leverage at the interface. The amount of behaviour a caller (or test) can exercise per unit of interface they have to learn. A module is deep when a large amount of behaviour sits behind a small interface, shallow when the interface is nearly as complex as the implementation.
Seam (Michael Feathers): a place where you can alter behaviour without editing in that place; the location at which a module's interface lives. Where to put the seam is its own design decision, distinct from what goes behind it. Avoid: boundary (overloaded with DDD's bounded context).
Adapter: a concrete thing that satisfies an interface at a seam. Describes role (what slot it fills), not substance (what's inside).
Leverage: what callers get from depth. More capability per unit of interface they learn. One implementation pays back across N call sites and M tests.
Locality: what maintainers get from depth. Change, bugs, knowledge, and verification concentrate in one place rather than spreading across callers. Fix once, fixed everywhere.
Deep module = small interface + lots of implementation:
┌─────────────────────┐
│ Small Interface │ ← Few methods, simple params
├─────────────────────┤
│ │
│ Deep Implementation│ ← Complex logic hidden
│ │
└─────────────────────┘
Shallow module = large interface + little implementation (avoid):
┌─────────────────────────────────┐
│ Large Interface │ ← Many methods, complex params
├─────────────────────────────────┤
│ Thin Implementation │ ← Just passes through
└─────────────────────────────────┘
When designing an interface, ask:
Good interfaces make testing natural:
Accept dependencies, don't create them.
// Testable
function processOrder(order, paymentGateway) {}
// Hard to test
function processOrder(order) {
const gateway = new StripeGateway();
}
Return results, don't produce side effects.
// Testable
function calculateDiscount(cart): Discount {}
// Hard to test
function applyDiscount(cart): void {
cart.total -= discount;
}
Small surface area. Fewer methods = fewer tests needed. Fewer params = simpler test setup.
interface keyword or a class's public methods: too narrow: interface here includes every fact a caller must know.This skill is written to stay usable across GitHub Copilot, Claude Code, and Codex.
$CODEX_HOME/skills/codebase-design and restart Codex after major changes.Preferred MCP Server: None required
codebase-design outside its documented task boundary.Before claiming the codebase-design workflow succeeded:
まだレビューはありません。使ってみた感想をお寄せください。
概要と使いどころ
AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.
日本語の概要は準備中です。原文の説明を表示しています。
Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and
日本語の概要は準備中です。原文の説明を表示しています。
12-agent academic paper writing pipeline. 11 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure/rebuttal-audit). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX-via-Pandoc/PDF output. Style Calibration + Writing Quality Check + Anti-Patterns with IRON RULE markers. Triggers: write paper, academic paper, guide my paper, parse reviews, audit my rebuttal, check my response draft, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見, 評估回覆, 논문 작성, 초록 작성, 논문 수정, 논문 계획을 도와줘, 심사 의견 반영, 답변서 점검, AI 사용 고지.
日本語の概要は準備中です。原文の説明を表示しています。
Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like 'write the paper from this outline,' 'compose the full manuscript,' 'execute the outline,' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.
日本語の概要は準備中です。原文の説明を表示しています。
Multi-perspective academic paper review with dynamic reviewer personas. Runs a 5-seat, role-separated review panel (Journal-Fit Reviewer + 3 peer-review roles + Devil's Advocate) with field-specific expertise; role separation is not a claim of independent error processes. Supports full review, re-review (verification), quick assessment, methodology focus, Socratic guided, and calibration modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review, calibrate reviewer, reviewer calibration, measure reviewer accuracy, 審查論文, 論文審查, 模擬審查, 同儕審查, 幫我審這篇, 以審查人角度評估, 審查者校準, 논문 심사, 동료 심사, 모의 심사, 심사자 관점에서 평가, 심사자 보정.
日本語の概要は準備中です。原文の説明を表示しています。
Systematic strategic planning framework for philosophy and interdisciplinary academic papers targeting preprint platforms (PhilArchive, arXiv, PhilSci-Archive). Use when users want to: (1) plan a paper on a specific topic, (2) identify research gaps and assess originality, (3) develop optimized paper outlines, (4) prepare for preprint submission, or (5) understand platform requirements and writing standards. Triggered by phrases like 'plan a paper on,' 'help me design a paper about,' 'identify research gaps in,' 'is this idea original,' or when users need structured research planning. The skill guides through three phases: Platform Analysis (identifying target venue and studying sample papers), Theoretical Framework (AI-driven literature search and gap identification), and Outline Optimization (structured design with reviewer-perspective self-assessment). Each phase includes quality evaluation standards and validation checkpoints.
日本語の概要は準備中です。原文の説明を表示しています。