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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.

80

Quality

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SKILL.md
Quality
Evals
Security

Quality

Content

100%

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

A tight, executable skill body that walks through method choice, Gibson and Golden Gate design with runnable commands, an explicit pre-order QC checkpoint, and gotchas — supported by a real QC script. It assumes Claude's competence while remaining fully actionable.

DimensionReasoningScore

Conciseness

The body is lean — it assumes Claude already knows what Gibson/Golden Gate are and uses tight tables and bullets with no padding about basic molecular biology. It is not a 2 because every section earns its tokens rather than including unnecessary explanation.

3 / 3

Actionability

Provides copy-paste-ready executable `tu run` commands with full JSON arguments and named output fields, plus a real referenced QC script with documented usage. It is not a 2 because the guidance is fully executable rather than pseudocode or abstract direction.

3 / 3

Workflow Clarity

Clear sequenced workflow (Step 0 method choice through Step 4 gotchas) with an explicit validation checkpoint at Step 3 ('QC before ordering', PASS/WARN) before the costly ordering step. It is not a 2 because an explicit feedback loop is present for this batch/risky operation.

3 / 3

Progressive Disclosure

Well-organized sections with a one-level-deep reference to a real bundle script (scripts/cloning_qc.py for QC details) and Related-skills links; for a sub-50-line body this satisfies the simple-skill allowance. It is not a 2 because navigation is clearly signaled and content is appropriately split rather than inlined.

3 / 3

Total

12

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12

Passed

Description

100%

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

A precise, third-person description that names concrete Gibson/Golden Gate capabilities, provides explicit 'Use when' triggers, and cleanly distinguishes itself from the companion primer-design skill. It answers both what and when without padding.

DimensionReasoningScore

Specificity

Lists multiple concrete capabilities — 'Gibson Assembly (overlap design for seamless multi-fragment joining)' and 'Golden Gate Assembly (Type IIS / BsaI / BbsI design with unique 4-bp fusion overhangs)' plus domestication, overhang-uniqueness, and overlap-Tm rules. It is not a 2 because it enumerates comprehensive specific actions rather than naming only the domain.

3 / 3

Completeness

Explicitly states both what ('Gibson/Golden Gate design', 'domestication', 'overhang-uniqueness', 'overlap-Tm') and when ('Use when you need to plan how to join DNA fragments... design assembly overlaps/overhangs, or decide between cloning methods'). It is not a 2 because the 'when' is an explicit trigger clause, not merely implied.

3 / 3

Trigger Term Quality

Includes natural terms a cloning user would say — 'Gibson Assembly', 'Golden Gate Assembly', 'plan how to join DNA fragments into a construct', 'design assembly overlaps/overhangs', 'cloning methods'. It is not a 2 because coverage spans the common variations rather than a single keyword.

3 / 3

Distinctiveness Conflict Risk

Occupies a clear molecular-cloning niche and explicitly distinguishes itself from the primer-design skill ('For PCR primers... see tooluniverse-primer-design'), so it is unlikely to trigger for the wrong skill. It is not a 2 because the triggers are specific and non-overlapping with sibling skills.

3 / 3

Total

12

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12

Passed

Validation

100%

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

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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