Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add K-Dense-AI/scientific-agent-skills --skill waypoint-biogit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/waypoint-bio)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/waypoint-bio"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/waypoint-bio/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/waypoint-bio"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/waypoint-bio.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Snyk pass
- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Excessive Agency · line 60 Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00130 | $0.03664 |
| Opus 5 | $0.00065 | $0.01832 |
| Sonnet 5 | $0.00026 | $0.00733 |
| Haiku 4.5 | $0.00013 | $0.00366 |
Grade A, and why
waypoint-bio scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 291 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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:
| 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 a downstream classifier.
- Fine-tuning a Waypoint checkpoint to predict a phenotype, treatment, or continuous readout from community composition.
- Scoring your own microbiome model against Compass so the number is comparable to the paper.
- Pretraining a taxonomic language model on Atlas or on your own corpus.
- Converting profiler output (MetaPhlAn, Kraken2/Bracken, QIIME 2, MGnify TSVs) into the input format these tools expect.
Do not reach for this when you have fewer than ~1,000 labelled samples — see Scientific caveats. A random forest on relative abundances is the better tool there, and the paper says so.
Setup
pip install waypoint-bio # installs the `waypoint` command
Atlas, Compass, and every Waypoint checkpoint are gated. Access is auto-approved, but you must click through once per repo and then authenticate:
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 291 lines · 130 tokens per session scan A 1fe859972d64
waypoint-bio is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed today), licensed MIT. It adds 130 tokens to every session and 3,664 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
bio-prefect-dask-nextflow
Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.
discovery-toolbox
A routed repertoire of 90 scientific thinking operators for biological research agents - visual reasoning, detectability and information budgets, search reframing, causal identification, competing explanations, observation and selection processes, pipeline artifact diagnosis, effort allocation, and confirmation…
rdkit-qsar-pharmacophore
Computes 2048-bit ECFP4 Morgan fingerprints from SMILES, trains LightGBM regressors for pIC50 prediction, and extracts SHAP feature attributions.
discovery-director
Operate as a research director making original discoveries from a given biological question and dataset. Use when the task is open-ended scientific research, exploring omics or experimental data for findings, hypothesis generation and testing, screening a large candidate space of genes, variants, features or…
bulk-rnaseq-counts-to-de-deseq2
Run differential expression analysis on bulk RNA-seq count data with DESeq2 (R). Covers DESeqDataSet construction from a count matrix, tximport (Salmon/Kallisto), featureCounts, or SummarizedExperiment; pre-filtering; design formulas (simple, batch, paired, interaction, multi-factor, LRT); result extraction by…
seurat-skill
Comprehensive Seurat v5 (R) guide for single-cell RNA-seq and multimodal analysis. Covers installation, standard workflows (Normalize/SCTransform), clustering, integration (CCA/RPCA/Harmony), differential expression (FindMarkers/FindAllMarkers), visualization (DimPlot/FeaturePlot/VlnPlot/DoHeatmap), spatial…