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p123p2000/synbio-igem-skills

Transforms synthetic biology research ideas, iGEM projects, courses, or science outreach needs into an executable blueprint with dependencies, evidence gates, and acceptance criteria. Suitable for planning, design, and retrospective; does not verify scientific conclusions or current-year competition rules.

What is synbio-igem-skills?

This AI agent skill is designed to help developers, researchers, and educators in synthetic biology and iGEM projects convert abstract ideas into structured, actionable plans. It emphasizes a dependency-aware, evidence-gated approach to ensure teams focus on validating the most critical unknowns first. The skill supports multiple blueprint types—research projects, courses, and outreach events—each with dedicated templates and references. It enforces clear separation of external facts from team decisions, scientific evidence from assumptions, and provides systematic rules for task granularity, dependency tracking, and risk management. The skill itself acts as a planning orchestrator, optionally collaborating with other specialist skills like synbio-expert and igem-mentor for deeper evidence support. Outputs are designed for immediate execution, with compressed summaries available for quick reviews, and integration with classroom platforms like OpenMAIC is supported for generating course briefs.

Works with~Claude Code~Codex CLI~Cursor
npx skills add https://github.com/p123p2000/synbio-igem-skills/tree/HEAD/skills/synbio-planner

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Documentation

Synthetic Biology Execution Blueprint

The goal of planning is not to expand an idea into a long document, but to let the team know what to verify first, who depends on whom, what evidence is sufficient to proceed, and when to change course.

Select Blueprint Type

Three Views to Complete Planning

Establish three corresponding views for the selected task; small tasks can be combined for presentation, but their logic must not be lost.

1. Outcome Map

Clearly describe the target audience, the desired change, observable outcomes, and acceptance methods. Treat "conducting experiments, running events, creating courseware" as tasks, not as effects themselves.

2. Dependency Map

List each item with: responsible role, inputs, resources, prerequisites, and deliverables. Mark as dependencies when budget, equipment, collaborations, approvals, and personnel are not yet confirmed; do not pretend they are already available.

3. Evidence Gates

For each critical phase, write: conditions to continue, conditions to pause, sources that need review, and alternative paths. Estimates must retain assumptions and formulas; simulated data, mock interviews, and sample outcomes must be clearly labeled as educational simulations.

Planning Rules

  1. First extract the time, personnel, capabilities, resources, audience, and constraints already provided by the user, then fill in reversible working assumptions.
  2. Separate external facts from team decisions. Scientific evidence must be supported by original papers or authoritative institutional materials; iGEM eligibility, fees, time, and safety requirements must be verified against the corresponding year's official sources.
  3. Task granularity should be suitable for handover and acceptance. Each task must at least answer: "Who, what to deliver, what it depends on, how to determine completion."
  4. First arrange a small-scale verification that exposes the main unknowns, then decide whether to expand. The purpose and passing criteria of the small-scale verification must be written in advance.
  5. When changing goals, simultaneously check dependencies, budget, evaluation methods, and risk register; avoid modifying only the title or summary.
  6. Biological plans only provide conceptual and managerial design commensurate with the task. Dangerous organisms, hazard enhancement, or detection evasion content must not be converted into executable optimization steps.

Output and Collaboration

Deliver a blueprint ready to start work: scope, three views, near-term tasks, pending items, and review milestones. When the user wants a condensed version, compress the presentation without mechanically filling in the template.

Other Skills are optional collaborators: synbio-expert provides evidence cards; igem-mentor provides current-year competition evidence; synbio-knowledge-base stores traceable materials; synbio-video and synbio-cue-cards handle explicitly requested delivery outputs. When these are missing, retain the interface fields and continue completing the current blueprint; do not claim the call was successful.

When submitting to classroom platforms such as OpenMAIC, output a course brief in the format: "Audience—Learning Outcomes—Chapters—Interactions—Quizzes—Sources—Non-Extrapolation Items". After the platform generates the page, content review is still required. Maintenance and reference scope can be found in Source Notes.

Individual skills in this repo

This repo contains 4 individual skills — each has its own dedicated page.

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