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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.

70

Quality

85%

Does it follow best practices?

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Adds up to 20 points to the overall score

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-molecular-cloning in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

75%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.

A well-structured, actionable skill body with concrete tool invocations, a method-selection table, and an explicit QC validation step. It earns solid 4s across the board, held back from 5s by minor redundancy in the Gotchas, placeholder sequences in examples, an implicit rather than explicit feedback loop, and an essentially monolithic overview.

Suggestions

Make the QC feedback loop explicit, e.g. 'If cloning_qc.py flags WARN, fix the flagged internal site / non-unique overhang / low-Tm overlap, then re-run QC until PASS before ordering.'

Replace the '…' placeholder fragments in the example commands with short but complete nucleotide strings so the snippets are runnable verbatim, or add a one-line note that ellipses abbreviate full sequences.

Trim the Step 4 Gotchas entries that merely restate Step 1/2 design rules, keeping only the higher-order failure guidance to reduce redundancy.

DimensionReasoningScore

Conciseness

Lean and assumes Claude's competence, but the Step 4 'Gotchas' section restates the internal-site, non-unique-overlap, repeat, and Tm-imbalance rules already covered in the Step 1/2 design rules, adding minor redundancy.

4 / 5

Actionability

Concrete, copy-paste-ready 'tu run' commands with full JSON argument structure and documented return fields (left_overlap, parts_with_overhangs), but the example fragment strings use '…' placeholders so the snippets are not runnable verbatim — a minor gap.

4 / 5

Workflow Clarity

Clear Step 0→4 sequence with an explicit QC validation checkpoint (scripts/cloning_qc.py flags PASS/WARN), but the validate→fix→retry feedback loop is only implied rather than spelled out.

4 / 5

Progressive Disclosure

Well-organized into labeled sections with QC logic appropriately extracted into a real, clearly signaled one-level-deep script (scripts/cloning_qc.py, verified present); most content is appropriately placed with only minor organization gaps.

4 / 5

Total

16

/

20

Passed

Description

95%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.

A strong, specific description with concrete actions, natural trigger terms, and an explicit 'Use when' clause that also disambiguates from a sibling primer-design skill. The only demerit is second-person voice ('you need'), which costs one specificity point per the voice guideline.

Suggestions

Rephrase the trigger clause in third person to avoid the voice penalty, e.g. 'Use when planning how to join DNA fragments into a construct…' instead of 'Use when you need to plan…'.

DimensionReasoningScore

Specificity

Lists multiple concrete actions (Gibson overlap design, Golden Gate overhang design, domestication, overhang-uniqueness, overlap-Tm rules), but the second-person phrasing 'Use when you need to plan…' triggers the voice penalty, lowering it from 5.

4 / 5

Completeness

Explicitly answers both 'what' (both assembly methods and their design rules) and 'when' via a concrete 'Use when you need to plan how to join DNA fragments…' trigger clause.

5 / 5

Trigger Term Quality

Comprehensive natural terms a molecular biologist would say — 'molecular cloning', 'Gibson Assembly', 'Golden Gate Assembly', 'join DNA fragments into a construct', 'cloning methods' — plus synonyms Type IIS/BsaI/BbsI.

5 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (assembly-junction design) and explicitly redirects primer design to the sibling tooluniverse-primer-design skill, minimizing overlap and conflict risk.

5 / 5

Total

19

/

20

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

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