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fair-esm2

Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.

72

Quality

91%

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SecuritybySnyk

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SKILL.md
Quality
Evals
Security

Quality

Content

93%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 dense, executable skill body that leads with working code, disambiguates the fair-esm package cleanly, and structures remote compute with a real submission flow. The only gap is the absence of an explicit validation/retry loop for the batch embedding workflow.

Suggestions

Add an explicit validation checkpoint after embeddings are saved (e.g., assert embeddings.pt loads and has the expected shape) to close the feedback loop on the batch compute workflow.

Resolve the `environment=...` placeholder with a concrete note on how the env name is selected from compute_details, so the remote-compute example is fully copy-paste ready.

DimensionReasoningScore

Conciseness

Lean and efficient — code-first with no padding of concepts Claude already knows; every section (prerequisites, embeddings, scoring, contacts, models, remote compute, troubleshooting) earns its place.

5 / 5

Actionability

Fully executable copy-paste Python for all three use cases plus a concrete submit_job remote-compute block; the only soft spot is `environment=...` left as a placeholder, but it explicitly defers to compute_details rather than guessing.

5 / 5

Workflow Clarity

The remote-compute flow is clearly sequenced (create → submit → wait_for_notification → save_artifacts → attach_job) with an implicit completion checkpoint via the notification, but lacks an explicit validate-then-retry feedback loop for the batch embedding job.

4 / 5

Progressive Disclosure

Well-organized overview with clearly signaled one-level-deep references to sibling skills (esmfold2, remote-compute-ssh, remote-compute-modal) and no bundle files needed; the skill is compact and appropriately self-contained.

5 / 5

Total

19

/

20

Passed

Description

88%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 that concretely states both capabilities and a numbered 'Use when' trigger list, with proper third-person voice. It is slightly technical in its trigger phrasing and has minor overlap risk with adjacent ESM skills.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — 'Extracting per-residue or per-sequence embeddings', 'Masked-LM likelihood / mutation effect scoring', 'Contact prediction' — giving comprehensive coverage of ESM-2 capabilities.

5 / 5

Completeness

Explicitly answers what ('Embed proteins with Meta AI's ESM-2') and when ('Use this skill when: (1)... (2)... (3)...') with concrete numbered trigger phrases.

5 / 5

Trigger Term Quality

Natural terms like 'Embed proteins', 'embeddings', 'mutation effect scoring', 'Contact prediction' are present and domain-appropriate, but it leans slightly technical and omits common lay synonyms a user might say.

4 / 5

Distinctiveness Conflict Risk

The fair-esm package naming and ESM-2 specifics carve a clear niche, but the protein-embedding space has closely related skills (e.g., the esmfold2 fork it disambiguates against), leaving minor overlap risk.

4 / 5

Total

18

/

20

Passed

Validation

81%

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

Validation13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

metadata_field

'metadata' should map string keys to string values

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

13

/

16

Passed

Repository
UnicomAI/wanwu
Reviewed

Table of Contents

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