awslabs/hcls-agent-skills is a collection of reusable instructions that help AI agents handle healthcare and life sciences work, including genomics, medical imaging, claims, and drug discovery. It is intended for agents running on Agent Skills-compatible platforms, and the catalogue entries are its individual domain skills.
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 awslabs/hcls-agent-skills --skill bioinformatics-on-healthomicsgit clone --depth 1 https://github.com/awslabs/hcls-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/awslabs/hcls-agent-skills/bioinformatics-on-healthomics)<a href="https://agentmods.dev/skills/awslabs/hcls-agent-skills/bioinformatics-on-healthomics"><img src="https://agentmods.dev/badge/skills/awslabs/hcls-agent-skills/bioinformatics-on-healthomics/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/awslabs/hcls-agent-skills/bioinformatics-on-healthomics"><img src="https://agentmods.dev/badge/skills/awslabs/hcls-agent-skills/bioinformatics-on-healthomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00199 | $0.04881 |
| Opus 5.5 | $0.00080 | $0.01952 |
| Sonnet 5.5 | $0.00040 | $0.00976 |
| Haiku 4.5 | $0.00020 | $0.00488 |
Grade A, and why
bioinformatics-on-healthomics 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 1mo 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.
The source is not reproduced here
Licensed MIT-0
The repository is licensed MIT-0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.
What ships with it
2 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.
- 1mo ago First seen · 483 lines · 199 tokens per session scan A e29cec8bce79
bioinformatics-on-healthomics is a skill published in the GitHub repository awslabs/hcls-agent-skills (65 stars, last pushed 15d ago), licensed MIT-0. It adds 199 tokens to every session and 4,881 once invoked, about $0.0008 per session on Opus 5.5. 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 2026-09-18.
Other skills, from other repositories
snakemake-workflow-engine
Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow…
nextflow-workflow-engine
Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized…
simpleitk-image-registration
Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal. Rigid/affine/deformable registration, threshold/region-growing segmentation, Gaussian/morph filtering, label stats, format conversion. Use to align volumes across timepoints/modalities, segment…
spatial-mapping-tangram
Tangram (tangram-sc) mapping of scRNA-seq onto spatial transcriptomics (Visium, Slide-seq, MERFISH, Xenium), one skill for every Tangram task: marker training genes, cells/clusters/constrained mode, per-spot cell type proportions, held-out gene validation (training scores, comparespatialgeneexp, AUC, k-fold CV)…
spatial-transcriptomics-cell-cell-communication
Spatial cell-cell communication / ligand-receptor (LR) interaction analysis, one skill for every route: LIANA consensus ranking between annotated cell types, CellPhoneDB v5 permutation p-values, DEG method and spatial microenvironments, squidpy neighbourhood enrichment to keep spatially adjacent sender-receiver pairs…
trackpy-particle-tracking
Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI…