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。
Spec-driven development lifecycle — EARS requirements, technical design docs, implementation tracking, and contribution guidelines. Use when planning features, defining requirements, or managing project lifecycle.
インストールする前に、エージェントに与えられる指示の中身を確認できます。
Structured approach to software development ensuring requirements are clearly defined, designs are meticulously planned, and implementations are thoroughly documented with proper contribution practices.
Use symptom -> action triggers: when one matches, apply this skill and verify with the protocol below.
Project Planning & Requirements:
Repository Contributions:
Quality Assurance:
Maintain these artifacts throughout the project lifecycle:
| Artifact | Purpose | Location |
|---|---|---|
requirements.md | User stories and acceptance criteria in EARS notation | Project root or /docs/requirements/ |
design.md | Technical architecture, sequence diagrams, implementation considerations | Project root or /docs/design/ |
tasks.md | Detailed, trackable implementation plan | Project root or /docs/planning/ |
EARS = Easy Approach to Requirements Syntax
1. Universal Requirements Apply to all entities without condition
2. State-Driven Requirements Apply only in specific system states
3. Event-Driven Requirements Triggered by specific events
4. Optional-Feature Requirements Describing optional or conditional features
5. Unwanted Behavior Specifying what should not happen
6. AI-Agent Requirements Specifying agent-visible constraints, handoff evidence, and autonomous execution limits
# User Authentication Requirements
## Universal Requirements
- U-001: The system **shall** require users to provide an email address and password for login.
- U-002: The system **shall** validate email addresses using RFC 5322 format.
## Event-Driven Requirements
- E-001: **When** the user clicks "Forgot Password", the system **shall** send a password reset link to the registered email.
- E-002: **Upon** successful authentication, the system **shall** generate a session token valid for 24 hours.
## State-Driven Requirements
- S-001: **If** the user has enabled two-factor authentication, the system **shall** prompt for the verification code.
- S-002: **When** the account is locked due to too many failed attempts, the system **shall** unlock it after 30 minutes.
## Unwanted Behavior
- N-001: The system **shall not** reveal whether an email address is registered during password reset.
- N-002: The system **shall not** allow the same account to be used from more than 3 IP addresses simultaneously.
## Optional Features
- O-001: The system **may** support social login providers (Google, Facebook, GitHub).
## AI-Agent Requirements
- A-001: The agent **shall** report changed files, commands run, and unresolved risks before handoff.
requirement = id ":" [trigger ","] subject "shall" action "." ;
trigger = ("When" | "If" | "While" | "Upon") condition ;
id = ("U" | "E" | "S" | "N" | "O" | "A") "-" digit digit digit ;
const earsRequirement =
/^(?<id>[UESNOA]-\d{3}):\s(?:(?<keyword>When|If|While|Upon)\s(?<condition>.+?),\s)?(?<subject>The system|The user|The agent)\sshall\s(?<action>.+)\.$/;
High-level description of what this feature does and why it's needed.
User → Frontend → API Gateway → Service → Database
↓
Cache Layer
src/
├── components/
│ └── FeatureName/
│ ├── FeatureComponent.tsx
│ ├── SubComponent.tsx
│ └── styles.css
├── services/
│ └── featureService.ts
├── api/
│ └── featureApi.ts
└── types/
└── feature.types.ts
interface FeatureEntity {
id: string;
name: string;
status: 'active' | 'inactive';
createdAt: Date;
// ... other fields
}
interface CreateFeatureRequest {
name: string;
/* ... other fields */
}
interface CreateFeatureResponse {
id: string;
status: 'created';
}
| Error Code | HTTP Status | Description |
|---|---|---|
| FEATURE_001 | 409 | Feature name already exists |
| FEATURE_002 | 400 | Invalid feature data |
User → Frontend: Click "Create Feature"
Frontend → API: POST /api/features
API → Validator: Validate data
Validator → API: Valid / Invalid
API → Database: Insert feature
Database → API: Created
API → Frontend: Return feature ID
Frontend → User: Show success message
### Implementation Task Tracking
```markdown
# Tasks: [Feature Name] Implementation
## Phase 1: Foundation
- [ ] Confirm scope, dependencies, and agent boundaries
- [ ] Create data model and migration scaffold
## Phase 2: Core Functionality
- [ ] Implement core API or service path
- [ ] Add validation, errors, and persistence
## Phase 3: Frontend Integration
- [ ] Build main component
- [ ] Cover loading, empty, error, and success states
## Phase 4: Verification
- [ ] Add unit/integration/component tests for changed paths
- [ ] Run required verification commands and record evidence
## Phase 5: Release Notes
- [ ] Document behavior, migration, and user-facing changes
Full scaffold reference: `examples/feature-spec-example.md` or `scripts/create-spec-scaffold.ps1`.
Before claiming "skill applied successfully":
Before creating any PR or making changes:
## Pre-Submission Checklist
### Repository Understanding
- [ ] Read README.md for project overview
- [ ] Read CONTRIBUTING.md for contribution rules
- [ ] Reviewed issue and PR templates
- [ ] Checked for existing related issues or PRs
### Environment Setup
- [ ] forked repository (if required)
- [ ] cloned repository locally
- [ ] setup development environment
- [ ] installed all dependencies
### Development Standards
- [ ] Understand coding style conventions
- [ ] Familiar with branching strategy
- [ ] Aware of commit message conventions
- [ ] Know testing requirements
## Issue: [Brief Title]
### Type: [Feature Request / Bug Report / Question / Documentation]
### Priority: [Low / Medium / High / Critical]
### Description
[Detailed description of the issue or feature request]
### Reproduction Steps (for bugs)
1. [First step]
2. [Second step]
3. [Third step]
### Expected Behavior
[What should happen]
### Actual Behavior
[What actually happened]
### Environment
- OS: [e.g., Windows 10, macOS 12.5]
- Browser: [e.g., Chrome 120, Firefox 115]
- Version: [If applicable]
### Additional Context
[Any other information that might be helpful]
- Screenshots
- Error messages
- Logs
## Branch Naming Convention
### Feature Branches
`feature/[JIRA-TICKET]/[short-description]`
Examples:
- feature/PROJ-123/user-authentication
- feature/PROJ-456/dark-mode-support
### Bugfix Branches
`bugfix/[JIRA-TICKET]/[issue-description]`
Examples:
- bugfix/PROJ-789/login-redirect-loop
- bugfix/PROJ-321/memory-leak-report
### Hotfix Branches (production issues)
`hotfix/[JIRA-TICKET]/[critical-description]`
Examples:
- hotfix/PROJ-999/security-vulnerability
- hotfix/PROJ-888/database-down
### Release Branches
`release/v[major].[minor]`
Examples:
- release/v1.2.0
- release/v2.0.0
### Branch Protection Rules
- Protect `main` and `develop` branches
- Require pull request reviews (at least 1 approval)
- Require status checks to pass (CI builds, tests)
- Require branches to be up-to-date before merging
## Conventional Commit Format
<type>[optional scope]: <description>
[optional body]
[optional footer(s)]
### Commit Types
| Type | Purpose | Example |
|------------|--------------------------------|----------------------------------|
| `feat` | New feature | `feat(auth): add OAuth2 support` |
| `fix` | Bug fix | `fix(api): resolve null reference` |
| `docs` | Documentation only | `docs(readme): update setup guide` |
| `style` | Formatting/style (no logic) | `style(ui): fix indentation` |
| `refactor` | Code refactor (no feature/fix) | `refactor(svc): extract helpers` |
| `perf` | Performance improvement | `perf(db): add index on email` |
| `test` | Add/update tests | `test(auth): add unit tests` |
| `build` | Build system/dependencies | `build(ci): upgrade Node to v20` |
| `ci` | CI/config changes | `ci(github): add workflow for PRs`|
| `chore` | Maintenance/misc | `chore(deps): update packages` |
| `revert` | Revert commit | `revert: feat(login)` |
### Breaking Changes
feat(api)!: remove deprecated v1 endpoint
BREAKING CHANGE: v1 endpoints are no longer supported. Use v2.
### Good Commit Examples
feat(auth): add refresh token mechanism
fix(ui): resolve mobile navigation issue
docs(readme): update installation instructions
### Bad Commit Examples (Don't use)
update 2 fixed bug wip changes final work in progress
### Commit Workflow
```bash
# Stage changes
git add .
# Interactive staging (optional)
git add -i
# Commit with good message
git commit -m "feat(auth): implement OAuth2 login"
# Or use multi-line for body and footer
git commit -m "fix(db): optimize query performance
Added composite index on user_email and created_at
Reduced query time from 500ms to 50ms
Closes issue #123"
## Pull Request Checklist
### Before Submitting
- [ ] Branch is up-to-date with target branch
- [ ] Code compiles without errors
- [ ] All tests pass locally
- [ ] Linters pass without errors
- [ ] Documentation updated (README, API docs, code comments)
- [ ] Self-review completed
### PR Description
- [ ] Clear title following conventional commits
- [ ] Description explains "why" not just "what"
- [ ] Screenshots for UI changes included
- [ ] Breaking changes documented
- [ ] Related issues referenced (e.g., "Closes #123")
- [ ] Testing instructions provided
### Code Quality
- [ ] Follows project coding standards
- [ ] No commented-out code
- [ ] No console.log statements
- [ ] meaningful variable and function names
- [ ] No sensitive data exposed
### Testing
- [ ] New features tested
- [ ] Bug fixes verified
- [ ] Edge cases covered
- [ ] Manual testing completed as described
## Description
[Provide a brief description of the changes in this PR]
## Type of Change
- [ ] Bug fix
- [ ] New feature
- [ ] Breaking change
- [ ] Documentation
- [ ] Refactoring
- [ ] Performance improvement
## Issue
[Closes #xxx] or [Related to #xxx]
## Changes Made
### Main Changes
- [Describe the main changes implemented]
### Technical Details
[Any technical details reviewers should know]
### Breaking Changes
[Any breaking changes and migration steps]
## Testing
### Manual Testing Steps
1. [Step 1]
2. [Step 2]
### Automated Testing
- [ ] Unit tests added and passing
- [ ] Integration tests added and passing
- [ ] E2E tests added and passing
## Screenshots
[Include before/after screenshots for UI changes]
## Checklist
- [ ] I have read the contributing guidelines
- [ ] My code follows the project style guidelines
- [ ] I have performed a self-review
- [ ] I have commented my code appropriately
- [ ] Changes have no linting errors
- [ ] All tests are passing
- [ ] Changes do not break existing functionality
## two-stage review (spec compliance first, then code quality) Principles
### Be Constructive
- Focus on improving code, not criticizing it
- Provide specific examples and suggestions
- Ask questions rather than making demands
- Acknowledge good code and smart solutions
### Review Focus Areas
#### Correctness
- [ ] Logic is correct and handles edge cases
- [ ] Error handling is adequate
- [ ] No obvious bugs or race conditions
- [ ] API contracts are maintained
#### Code Quality
- [ ] Code is readable and maintainable
- [ ] Naming follows conventions
- [ ] Complexity is reasonable
- [ ] No code duplication
#### Architecture
- [ ] Follows established patterns
- [ ] Good separation of concerns
- [ ] Proper abstractions used
- [ ] No tight coupling
#### Security
- [ ] No security vulnerabilities
- [ ] Input validation present
- [ ] Authentication/authorization correct
- [ ] No sensitive data exposure
### Review Priority Comments
🔴 **Blocker**: Must be fixed before merge
🟡 **Concern**: Discuss before merge
🟢 **Suggestion**: Nice to have, not blocking
### [TYPE] - [ACTION] - [TIMESTAMP]
**Objective**: [Goal being accomplished]
**Context**: [Current state, requirements, reference to prior steps]
**Decision**: [Approach chosen and rationale]
**Execution**: [Steps taken with parameters and commands]
**Output**: [Complete results, logs, metrics]
**Validation**: [Success verification and results]
**Next**: [Continuation plan to next action]
### Decision - [TIMESTAMP]
**Decision**: [What was decided]
**Context**: [Situation and driving data]
**Options**:
- Option 1: [Description] - [Pros/Cons]
- Option 2: [Description] - [Pros/Cons]
- Option 3: [Description] - [Pros/Cons]
**Rationale**: [Why selected option is superior]
**Impact**: [Anticipated consequences]
**Review**: [Reassessment conditions]
Streamlined Action Log (for changelogs):
[TYPE][TIMESTAMP] Goal: [X] → Action: [Y] → Result: [Z] → Next: [W]
Quick Summary (for updates): What: [Brief description] Why: [Context/rationale] How: [Approach taken] Status: [Current state] Next: [Upcoming step]
## Definition of Done (DoD)
### Development
- [ ] Code written and committed
- [ ] Code follows project style guide
- [ ] Code compiles without errors
- [ ] No console errors or warnings
- [ ] Self-review completed
### Testing
- [ ] Unit tests written and passing
- [ ] Integration tests written and passing
- [ ] Manual testing completed
- [ ] Edge cases identified and handled
- [ ] Test coverage meets project threshold (>80%)
### Documentation
- [ ] README updated if API changed
- [ ] API documentation updated
- [ ] Code comments added/updated
- [ ] User documentation updated if needed
### two-stage review (spec compliance first, then code quality)
- [ ] Pull request created
- [ ] At least one approval received
- [ ] All review comments addressed
- [ ] CI/CD pipeline passes
- [ ] Merged to appropriate branch
### Deployment
- [ ] Deployment tested in staging
- [ ] Smoke tests passed
- [ ] Performance validated
- [ ] Monitoring/alerting configured
- [ ] Rollback procedure documented
## Code Quality Checklist
### Functionality
- [ ] All acceptance criteria met
- [ ] Requirements from design document fulfilled
- [ ] Edge cases handled
- [ ] Error states handled gracefully
### Usability
- [ ] User-friendly error messages
- [ ] Clear feedback for actions
- [ ] Accessible (keyboard, screen reader)
- [ ] Responsive design verified
### Performance
- [ ] Meet performance requirements
- [ ] No memory leaks
- [ ] Efficient algorithms used
- [ ] Appropriate caching
### Security
- [ ] Input validation
- [ ] Output encoding (prevent XSS)
- [ ] Authentication/authorization implemented
- [ ] No sensitive data in logs
- [ ] Dependencies audited and up-to-date
### Maintainability
- [ ] Code is readable
- [ ] Good variable/function names
- [ ] Appropriate abstractions
- [ ] No code duplication
- [ ] Adequate comments
### Testing
- [ ] Unit tests for critical paths
- [ ] Integration tests for API
- [ ] E2E tests for user flows
- [ ] Tests are reliable and not flaky
## Development Phases
### Phase 1: Requirements & Planning
- Gather requirements from stakeholders
- Document in EARS notation
- Create technical design
- Identify risks and dependencies
- Estimate effort and timeline
### Phase 2: Development
- Set up feature branches
- Implement core functionality
- Write tests alongside code
- two-stage review (spec compliance first, then code quality) and iteration
### Phase 3: Testing & QA
- Run automated tests
- Perform manual testing
- Conduct QA review
- Fix identified issues
- Performance testing
### Phase 4: Deployment
- Deploy to staging
- Execute smoke tests
- Get stakeholder approval
- Deploy to production
- Monitor for issues
### Phase 5: Post-Release
- Monitor metrics and logs
- Collect user feedback
- Address critical bugs
- Document lessons learned
- Update process improvements
This skill is written to stay usable across GitHub Copilot, Claude Code, and Codex.
$CODEX_HOME/skills/development-workflow and restart Codex after major changes.Preferred MCP Server: None required
SKILL.md, bundled references or scripts, and manual verification. Show the exact commands, evidence, and final checks you used before concluding."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。