tooluniverse-molecular-cloning

Molecular cloning assembly design — Gibson Assembly (overlap design for seamless multi-fragment joining) and Golden Gate Assembly (Type IIS / BsaI / BbsI design with unique 4-bp fusion overhangs). Use when you need to plan how to join DNA fragments into a construct, design assembly overlaps/overhangs, or decide between cloning methods. Covers the domestication (internal-site removal), overhang-uniqueness, and overlap-Tm rules. For PCR primers to generate the fragments, see tooluniverse-primer-design.

Quality

95%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide

Securityby

Passed

No findings from the security scan

Quality

Content

90%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is tight, executable, and well-structured with a clear method-selection step, runnable commands, and an explicit QC checkpoint. The only minor gap is that the validate→fix→re-run feedback loop is implied via the QC script and gotchas rather than spelled out as an explicit loop.

Suggestions

In Step 3, make the feedback loop explicit: 'if any WARN, fix (domesticate / redesign overhang or overlap) and re-run cloning_qc.py until all PASS before ordering'.

Consider a short one-line 'See tooluniverse-primer-design' pointer inside the Gibson step where `with_overlaps` is handed off, to make the inter-skill handoff more discoverable inline.

Dimension	Reasoning	Score
Conciseness	Lean and efficient throughout: a compact method-selection table, copy-paste commands, and bulleted rules with no padding about what DNA/cloning is. Every token earns its place.	5 / 5
Actionability	Fully executable: real `tu run` invocations with concrete JSON args, explicit design rules, and a bundled `scripts/cloning_qc.py` with usage examples covering the common cases.	5 / 5
Workflow Clarity	Clear Step 0–4 sequence with an explicit QC checkpoint (Step 3 runs cloning_qc.py flagging PASS/WARN) and a gotchas section for error recovery; slightly short of a fully stated validate→fix→re-run feedback loop in prose.	4 / 5
Progressive Disclosure	Well-organized sections with a real one-level bundle reference (scripts/cloning_qc.py, verified to exist) and sibling-skill pointers; no nested references, though it lacks formal deep-dive .md links for advanced detail.	4 / 5
	Total	18 / 20 Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is specific, complete, and distinct: it states concrete capabilities, gives explicit 'Use when' triggers with natural vocabulary, and cleanly separates its scope from the related primer-design skill. No vague fluff or over-claims.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions—'design the overlaps (Gibson) or Type IIS overhangs (Golden Gate)', 'domestication (internal-site removal), overhang-uniqueness, and overlap-Tm rules'—covering the domain comprehensively.	5 / 5
Completeness	Explicitly answers both what (design overlaps/overhangs, domestication, uniqueness, Tm rules) and when ('Use when you need to plan how to join DNA fragments into a construct, design assembly overlaps/overhangs, or decide between cloning methods').	5 / 5
Trigger Term Quality	Comprehensive natural terms users would actually say: 'Molecular cloning assembly design', 'Gibson Assembly', 'Golden Gate Assembly', 'Type IIS / BsaI / BbsI', 'join DNA fragments into a construct', and 'decide between cloning methods'.	5 / 5
Distinctiveness Conflict Risk	Clear niche (cloning assembly design) with distinct triggers; explicitly distinguishes itself from the adjacent tooluniverse-primer-design skill, minimizing conflict risk.	5 / 5
	Total	20 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: mims-harvard/ToolUniverse
Path: plugin/skills/tooluniverse-molecular-cloning/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

Table of Contents

Discovery Implementation Validation

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.