synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and 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 synthetic-sciences/openscience --skill pathogen-variant-surveillancegit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote 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/synthetic-sciences/openscience/pathogen-variant-surveillance)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/pathogen-variant-surveillance"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/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/synthetic-sciences/openscience/pathogen-variant-surveillance"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/pathogen-variant-surveillance.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 | $0.00249 | $0.03459 |
| Opus 5.5 | $0.00100 | $0.01384 |
| Sonnet 5.5 | $0.00050 | $0.00692 |
| Haiku 4.5 | $0.00025 | $0.00346 |
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 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.
This is a copy
100% identical to pathogen-variant-surveillance — 259 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 233 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.
- 1mo ago Changed · +5 lines 5ade26b893a8
- 1mo ago First seen · 228 lines · 249 tokens per session scan A 71ad92429e10
pathogen-variant-surveillance is a skill published in the GitHub repository synthetic-sciences/openscience (4,025 stars, last pushed today), licensed Apache-2.0. It adds 249 tokens to every session and 3,459 once invoked, about $0.0010 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 100% identical to pathogen-variant-surveillance, differing in 259 lines, and is treated as a copy.
Other skills, from other repositories
songsee
Audio spectrograms/features (mel, chroma, MFCC) via CLI.
arxiv
Search arXiv papers by keyword, author, category, or ID.
research-paper-writing
Write ML papers for NeurIPS/ICML/ICLR: design→submit.
paper-revision-author
Revise independently drafted paper sections into one coherent LaTeX body before the abstract is written.
paper-plot-stub
Plot a results CSV (x, ybaseline, yours) as a two-line matplotlib chart and write a PDF. Demo-only.
knowledge-extension-ecosystem-lsp-code-intelligence
A codebase guide to LSP, the standard protocol behind editor features such as symbol queries, file diagnostics, and language-aware code information.