waypoint-bio SKILL.md skillA
waypoint-bio from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/waypoint-bio@v1.3Pins v1.3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/waypoint-bio/SKILL.md- Versions recorded
- 4
- Latest version
- v1.3, committed Oct 1, 2026
- First version recorded
- Aug 17, 2026
- Size
- 16,666 bytes
- Repository stars
- 56,497
- License
- MIT
Supports work 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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Waypoint: Outpost Bio's Open Microbiome Foundation Models ## Overview Outpost Bio open-sourced three artefacts under Apache 2.0, described in [Treloar et al., bioRxiv 2026.05.02.722381](https://www.biorxiv.org/content/10.64898/2026.05.02.722381v2): | Artefact | What it is | Hugging Face | | --- | --- | --- | | **Waypoint** | GPT-2-style causal LMs over taxonomic tokens, 6M–170M params | `outpost-bio/Waypoint-6m`, `-45m`, `-170m` | | **Atlas** | 539,308 microbiome samples scraped from MGnify (485,377 pretrain / 53,931 benchmark) | `outpost-bio/Atlas` | | **Compass** | Eight downstream tasks over four studies | `outpost-bio/Compass` | The unifying idea: a microbiome sample is a *sentence*. Each taxon is one token, tokens are ordered by descending abundance z-score, and the model is trained with next-token prediction. A pretrained checkpoint then supplies sample-level embeddings or a fine-tuning backbone for prediction tasks. All of it is driven by one CLI, `waypoint`, with five subcommands: `prepare-dataset`, `embed`, `finetune`, `benchmark`, `pretrain`. ## When to use - Embedding 16S/shotgun taxonomic profiles into fixed-size vectors for clustering, visualisation, or …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/waypoint-bio@sha256:132d1f33d5d99bd6The line at the top of this page pins the label v1.3, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_ktmktzlztfqmetyc)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Aug 17, 2026 and Oct 1, 2026, about one every 15 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.3 latest | 2026-10-01 | a92663a | 16,666 B | A | view · diff |
| v1.2 | 2026-09-30 | ce9e6e9 | 14,406 B | A | view · diff |
| v1.1 | 2026-09-02 | 1e5eeff | 14,093 B | A | view · diff |
| v1.0 | 2026-08-17 | 204eef5 | 13,135 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16666 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ktmktzlztfqmetyc GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/waypoint-bio GET https://markdownregistry.com/api/v1/blob/132d1f33d5d99bd6288a4cb432b277fcbc0f8bc4315e333dcecb840e7adc87a5
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.