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tooluniverse-computational-biophysics

Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), toxicology (LD50, NOAEL), population genetics (Hardy-Weinberg, Fst), enzyme kinetics (Michaelis-Menten), thermodynamics. Use for first-principles quantitative biology calculations, dose calculations, exposure assessment, and biophysical-property estimation.

Quality

85%

Does it follow best practices?

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

67%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, highly actionable skill body: every bundled script has concrete usage examples, formulas are stated explicitly, and verification habits are built into the compute and MC workflows. The main costs are token weight from textbook-style concept explanations and test-taking trivia, and script path references that do not match the actual bundle layout.

Suggestions

Trim or compress background explanations of well-known concepts (exponential decay, Kd meaning, generic MC heuristics like 'the longest option is correct more often') to lift conciseness toward level 5.

Expand Templates 2, 3, 5, 6, and 7 from one-line formulas into short runnable snippets, matching the standard Template 1 already demonstrates, to make actionability uniformly copy-paste ready.

Fix script paths to the actual bundle layout ('scripts/...' rather than 'skills/tooluniverse-computational-biophysics/scripts/...') and consider moving the script catalog and MC strategy sections into reference files to slim SKILL.md.

DimensionReasoningScore

Conciseness

The body is dense and mostly earns its tokens (templates, exact CLI invocations, formulas), but several passages explain concepts Claude already knows — e.g. 'Kd = concentration at half-maximal binding', 'Radioactive tracer decays over time... Same math as drug elimination', and general MC test-taking trivia like 'All/None of the above is correct only ~25% of the time' and 'The longest/most detailed option is correct more often'. This fits the level-3 anchor ('mostly efficient but includes some unnecessary explanation or could be tightened'); it is above level 2 because padding is incidental, not pervasive, and below level 4 because multiple sections could be trimmed without losing actionability.

3 / 5

Actionability

Most guidance is copy-paste ready: full invocation lines with flags for every bundled script ('python epidemiology.py --type r0_herd --R0 3.5 --VE 0.90'), a complete Template 1 with executable functions, and concrete tool names for lookups. It falls short of level 5 because several computation templates (Templates 2, 3, 5, 6, 7) are one-line formulas or prose rather than the executable code the section itself mandates, and the mc_analyzer.py usage block omits the script's output contract.

4 / 5

Workflow Clarity

Sequences are clear and include explicit validation checkpoints: the section-4 pattern ('1. Extract ALL given values... 5. VERIFY: substitute your answer back into the original problem'), the MC process with forced elimination and letter-to-text verification, and pitfalls to flag. It does not reach level 5 because there is no unified end-to-end workflow (decision points are scattered across sections 3-8), the claimed script-level verification steps are asserted but never demonstrated, and there is no explicit fix-and-retry feedback loop.

4 / 5

Progressive Disclosure

SKILL.md serves as an overview with per-script documentation pointing to real bundled files (all nine referenced scripts exist in scripts/), and each script's details are appropriately left to the file itself. Minor gaps keep it below level 5: the body cites the non-bundled path prefix 'skills/tooluniverse-computational-biophysics/scripts/' instead of the actual 'scripts/' location, and sections 5-7 are long enough (MC strategy, script catalog) that some material could live in reference files.

4 / 5

Total

15

/

20

Passed

Description

96%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 description: it names concrete capabilities with domain-specific quantities, includes natural trigger terms, and explicitly answers both what the skill does and when to use it. The only weakness is breadth across many quantitative-biology sub-disciplines, which slightly raises conflict risk with more specialized single-domain skills.

DimensionReasoningScore

Specificity

The description enumerates concrete capabilities with named quantities: 'PK volume of distribution, clearance, half-life', 'R0, attack rate', 'LD50, NOAEL', 'Hardy-Weinberg, Fst', 'Michaelis-Menten'. This matches the level-5 anchor of multiple specific concrete actions with comprehensive coverage; it is not level 4 because there are no meaningful gaps in the domain's coverage.

5 / 5

Completeness

Both questions are explicitly answered: 'what' via 'Solve quantitative problems in biophysics — pharmacokinetics (...), epidemiology (...), toxicology (...)' and 'when' via the explicit trigger clause 'Use for first-principles quantitative biology calculations, dose calculations, exposure assessment, and biophysical-property estimation.' This mirrors the level-5 anchor example with a concrete 'Use for...' clause; it is not level 4 because the 'when' is already fully explicit, not merely improvable.

5 / 5

Trigger Term Quality

Natural terms users would actually say are comprehensively covered, including synonyms and domain shorthand: 'pharmacokinetics', 'half-life', 'dose calculations', 'exposure assessment', 'R0', 'Hardy-Weinberg', 'Michaelis-Menten'. This matches the level-5 anchor (comprehensive coverage including synonyms); it exceeds level 4 because even sub-domain vocabulary (Fst, NOAEL, LD50) is present.

5 / 5

Distinctiveness Conflict Risk

The niche is clear — first-principles quantitative biology calculations — and unlikely to trigger for, say, a literature-review or document skill. However, the breadth spans pharmacokinetics, epidemiology, toxicology, genetics, enzyme kinetics, and thermodynamics, each of which could have its own dedicated skill, creating minor overlap risk with single-domain skills. This fits the level-4 anchor ('mostly distinct; minor overlap risk'); it falls short of level 5 because that breadth dilutes the distinct-trigger claim.

4 / 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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-computational-biophysics/SKILL.md

Reviewed

Table of Contents

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