> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# waypoint-bio — AI agent skill for life sciences

> Use when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pre…

# `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.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** MIT · **Version:** 1.1

## Install

```bash theme={null}
npx research-agent-skills install waypoint-bio
npx skills add KalarisLabs/research-agent-skills --skill waypoint-bio
```

## When to use it

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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/waypoint-bio/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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