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waypoint-bio

Use when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus, the Compass eight-task benchmark, or the `waypoint` CLI from the `waypoint-bio` package. Covers embedding microbiome samples, fine-tuning on taxonomic abundance data, benchmarking a checkpoint on Compass, pretraining a GPT-2 model on taxonomic abundance profiles, and converting MetaPhlAn, Kraken2, QIIME 2, or MGnify abundance tables into waypoint format.

76

Quality

96%

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

92%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: copy-paste commands for every subcommand, a sequenced six-step workflow with an explicit pre-flight validation checkpoint, and clean progressive disclosure into four real reference files and two scripts. The only minor gap is a little explanatory prose that could be tightened without losing clarity.

DimensionReasoningScore

Conciseness

Mostly lean — tables, bullet lists, and code blocks carry the content, and the prose (the 'sentence' metaphor, pooling rationale, caveats) is novel 2026 domain knowledge Claude would not already know. A few explanatory passages around the code could be trimmed slightly, sitting just below the 'every token earns its place' anchor.

4 / 5

Actionability

Fully executable, copy-paste-ready commands with concrete flags across all five subcommands and both bundled scripts (e.g. 'waypoint embed --model outpost-bio/Waypoint-6m --data dataset.parquet --output embeddings.parquet'), covering the common embedding/finetune/benchmark/pretrain cases.

5 / 5

Workflow Clarity

A numbered six-step workflow (prepare → vocab coverage → embed → finetune → benchmark → pretrain) with an explicit validation checkpoint in step 2 ('Check vocabulary coverage before anything else', with the ~0.8 threshold and re-examine guidance) and a load-bearing caveats checklist, satisfying the explicit-validation/feedback-loop anchor.

5 / 5

Progressive Disclosure

SKILL.md is a concise overview that points to four real one-level-deep reference files (cli-reference.md, compass-benchmark.md, data-preparation.md, python-api.md) and two real scripts, all verified present and clearly signaled via dedicated References/Scripts sections plus inline 'See references/... for...' pointers.

5 / 5

Total

19

/

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.

A strong, third-person description that names the domain, enumerates five concrete capabilities, and opens with an explicit 'Use when...' trigger clause covering the specific artefacts and profilers involved. It is comprehensive and distinct with no vague fluff.

DimensionReasoningScore

Specificity

Lists five concrete actions — 'embedding microbiome samples, fine-tuning on taxonomic abundance data, benchmarking a checkpoint on Compass, pretraining a GPT-2 model on taxonomic abundance profiles, and converting MetaPhlAn, Kraken2, QIIME 2, or MGnify abundance tables into waypoint format' — giving comprehensive coverage of the domain's capabilities.

5 / 5

Completeness

Explicitly answers both: 'what' via 'Covers embedding... fine-tuning... benchmarking... pretraining... and converting...' and 'when' via the opening 'Use when working with Outpost Bio's open microbiome foundation models...', matching the anchor that requires concrete trigger phrases for both.

5 / 5

Trigger Term Quality

Comprehensive natural terms a domain user would actually say — 'microbiome foundation models', 'Waypoint checkpoints', 'Atlas pretraining corpus', 'Compass eight-task benchmark', 'waypoint CLI', plus profiler names (MetaPhlAn, Kraken2, QIIME 2, MGnify) as synonyms/entry points.

5 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (Outpost Bio's Waypoint/Atlas/Compass artefacts and the waypoint-bio package) with distinct triggers and minimal overlap risk with other skills.

5 / 5

Total

20

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_field

'metadata' should map string keys to string values

Warning

Total

15

/

16

Passed

Repository
K-Dense-AI/scientific-agent-skills
Reviewed

Table of Contents

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