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 pathogen-variant-surveillancegit 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/pathogen-variant-surveillance)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/pathogen-variant-surveillance"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/pathogen-variant-surveillance/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/pathogen-variant-surveillance"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/pathogen-variant-surveillance.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk warn
- NVIDIA SkillSpector pass
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 | $0.00249 | $0.03388 |
| Opus 5 | $0.00125 | $0.01694 |
| Sonnet 5 | $0.00050 | $0.00678 |
| Haiku 4.5 | $0.00025 | $0.00339 |
Grade A, and why
pathogen-variant-surveillance 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 8d 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- pathogen-variant-surveillance — 91% identical, 19 lines differ
How it starts
The opening of the file, as written. The whole thing — 226 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Pathogen Variant Surveillance
When to use
Any time an answer depends on what a pathogen population looks like now: which lineages are circulating, whether one is growing, what a lineage name currently means, or whether an assay target still matches.
The rule
Never state what is circulating, and never write a lineage name, from memory.
Three things go wrong at once, and only the first is an ordinary knowledge-cutoff problem:
- Names post-date training. The Pango designation list carries over 6,200 names and grows continuously.
- The nomenclature is a live data structure, not a convention.
XFGis a recombinant that only resolves throughalias_key.json;PQ.17unaliases toXDV.1.5.1.1.8.1.17. Neither expansion is derivable by reasoning — the mapping is a file that changes. - Prior knowledge gets retracted, not just outdated. 294 names in the current
lineage_notes.txtare withdrawn or redesignated.PC.2is nowLF.7.9;XFG.20was withdrawn outright. A remembered lineage fact is not merely stale, it can be actively wrong.
Every number this skill reports is a count returned by a live instance, stamped with the data version it came from.
Scope
Surveillance data analysis for research. This skill describes sequences that were collected and submitted; it does not produce clinical interpretations, outbreak-response recommendations, or public-health guidance, and sequence counts are not case counts.
Instances
One API shape covers every pathogen. --instance names a verified deployment; --base-url
reaches any other LAPIS instance.
| Instance | Host | Lineage column | Indexed |
|---|---|---|---|
sars-cov-2 |
lapis.cov-spectrum.org (open GenBank data) | pangoLineage |
yes |
h5n1, h3n2, h1n1pdm, influenza-a |
lapis.genspectrum.org | clade |
no |
rsv-a, rsv-b, mpox, measles, dengue, west-nile, hmpv, ebola-zaire, ebola-sudan, cchf |
lapis.pathoplexus.org | varies | varies |
What ships with it
8 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.
- references/lapis-api.md 9.5 KB
- references/lineage-nomenclature.md 6.3 KB
- references/surveillance-caveats.md 8.3 KB
- scripts/lapis_client.py 30 KB runs code
- scripts/lineage_prevalence.py 13 KB runs code
- scripts/mutation_profile.py 9.2 KB runs code
- scripts/reporting_lag.py 8.4 KB runs code
- scripts/resolve_lineage.py 7.0 KB runs code
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.
- 8d ago First seen · 226 lines · 249 tokens per session scan A 9db864de6bf1
pathogen-variant-surveillance is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed today), licensed MIT. It adds 249 tokens to every session and 3,388 once invoked, about $0.0012 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
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…
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…
polars-dovmed
Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.
bio-interdomain-hgt
Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.
csag-extraction
Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.
exploratory-data-analysis
Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.