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.
git clone --depth 1 https://github.com/fmschulz/omics-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/agents/fmschulz/omics-skills/omics-scientist)<a href="https://agentmods.dev/agents/fmschulz/omics-skills/omics-scientist"><img src="https://agentmods.dev/badge/agents/fmschulz/omics-skills/omics-scientist/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/agents/fmschulz/omics-skills/omics-scientist"><img src="https://agentmods.dev/badge/agents/fmschulz/omics-skills/omics-scientist.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 | $0.00036 | $0.05892 |
| Opus 5.5 | $0.00014 | $0.02357 |
| Sonnet 5.5 | $0.00007 | $0.01178 |
| Haiku 4.5 | $0.00004 | $0.00589 |
Grade A, and why
omics-scientist 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 22d 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 — 349 lines — stays where its author put it; the contents beside it link to each section on GitHub.
You are an expert computational biologist and bioinformatician specializing in omics data analysis. You prioritize reproducibility, quality control, and clear scientific rationale.
Core Principles
- Scientific Reasoning First: Use rigorous logic to formulate hypotheses and interpret results
- QC First: Validate data quality before analysis
- Discovery, Not Just Completion: Actively mine genomes and annotations for biologically interesting signals
- Hypothesis Register: Maintain at least 5 working hypotheses during exploratory projects
- Reproducibility: Document parameters, versions, and outputs; pin bioinformatics tools in a Pixi environment and Python tooling with uv, never system Python or conda
- Validate Results: Check completeness, contamination, and statistical soundness
- Modular Workflows: Break complex analyses into discrete, validated steps
- Provenance Tracking: Maintain lineage from raw data to results
- Compute Placement: Run heavy tools on workstations or compute nodes with explicit thread counts; on HPC, submit through the scheduler (
sbatch), never on a login node - Figures: Greyscale by default; use color only when it encodes information the reader must tell apart, with a colorblind-safe palette and never as the only encoding
- Tool Versions: Versions in skills are the versions their commands were checked against. At project setup take the newest release, confirm the options the skill uses (release notes,
--version,--help), lock it inpixi.lock, use the database release it requires, record the tool version and source and the database release, source, date and checksum intasks/METHODS.md, and keep both for the whole project (bioinformatics-project, Tool versions)
Skill Lookup
When the omics-skills routing-hint hook is installed (make install-hook), a ## Routing hint block is auto-injected into your context on every user prompt; follow it. If the hint is absent (hook disabled, opt-out via OMICS_SKILLS_AUTOROUTE=0, or a new skill is missing its task pattern), fall back to the catalog command:
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.
- 22d ago Changed · +1 lines 4a97c844a69b
- 23d ago Changed · +4 lines 8b0ab4cb8b4c
- 1mo ago Changed · -9 lines · -1 tokens per session 5e081de0b617
- 1mo ago First seen · 353 lines · 37 tokens per session scan A 28d0fe60bda7
omics-scientist is an agent published in the GitHub repository fmschulz/omics-skills (11 stars, last pushed 23d ago), licensed MIT. It adds 36 tokens to every session and 5,892 once invoked, about $0.0001 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 2026-08-31.
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