Open Science is a local-first, model-agnostic workbench for reproducible scientific research. Scientists use its AI agents, Python and R execution, data connectors, and traceable outputs for tasks such as literature review, analysis, simulation, and visualization across macOS, Windows, and Linux.
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 aipoch/open-science --skill scvi-toolsgit clone --depth 1 https://github.com/aipoch/open-scienceWrote 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/aipoch/open-science/scvi-tools)<a href="https://agentmods.dev/skills/aipoch/open-science/scvi-tools"><img src="https://agentmods.dev/badge/skills/aipoch/open-science/scvi-tools/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/aipoch/open-science/scvi-tools"><img src="https://agentmods.dev/badge/skills/aipoch/open-science/scvi-tools.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 15 findings, 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 Memory Poisoning · line 165 Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.Fix: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
- medium Memory Poisoning · line 167 Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.Fix: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
- medium Memory Poisoning · line 169 Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.Fix: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
- medium Memory Poisoning · line 170 Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.Fix: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
- medium Prompt Injection · line 165 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 166 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 167 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 169 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 170 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 174 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 174 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 176 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 178 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 179 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
- medium Prompt Injection · line 180 Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
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 | $0.00100 | $0.02860 |
| Opus 5.5 | $0.00040 | $0.01144 |
| Sonnet 5.5 | $0.00020 | $0.00572 |
| Haiku 4.5 | $0.00010 | $0.00286 |
Grade A, and why
scvi-tools 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- scvi-tools — 100% identical, 82 lines differ
How it starts
The opening of the file, as written. The whole thing — 206 lines — stays where its author put it; the contents beside it link to each section on GitHub.
scvi-tools — scVI / scANVI
scvi-tools (Gayoso et al. 2022, github.com/scverse/scvi-tools, BSD-3-Clause)
wraps a family
of deep generative models for single-cell omics. The scRNA-seq core is scVI
(unsupervised batch-corrected latent embedding) and scANVI (scVI + a
classifier head for semi-supervised cell-type label transfer). Both expect
raw integer UMI counts and emit a low-dimensional X_scVI / X_scANVI
that drops into the scanpy neighbors → leiden → umap pipeline.
Setup (any agent, no API key)
This is a pure skill — kernel.py is deterministic Python and you (the
base model) do all the reasoning. There is no host runtime and no LLM API.
The helpers are prepare_scvi_counts for input validation and h5ad_safe_obs
for obs/var frames that anndata.write_h5ad() can serialize. Load them once
per session in a Python cell:
exec(open("scvi-tools/kernel.py", encoding="utf-8").read()) # path to this skill's kernel.py
Nothing auto-loads it outside Claude Science. Then call the helpers directly.
If a helper raises NameError, you haven't exec'd kernel.py.
Dependencies: pip install scvi-tools scanpy anndata. Training needs a
CUDA-capable GPU — see Remote compute to fall out
to a rented GPU when you don't have one locally.
How to run
scVI — batch-corrected latent space
prepare_scvi_counts(adata) checks and preserves existing counts. If absent,
it checks .X before copying it to counts. Values must be finite, nonnegative,
and integer-valued, with at least one positive count. Invalid existing counts
raise instead of being replaced by .X; sparse matrices stay sparse.
These numerical checks cannot prove raw-count provenance. Check the dataset
documentation or preprocessing history; do not round or exponentiate transformed
values to make them pass. If the history is unclear, resolve it before training.
The helper does not use .raw.X, which may be normalized or have a different
gene axis. Use an in-memory AnnData object; materialize backed data or copy views
only within the available memory budget.
What ships with it
3 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 Changed · +18 lines 27779ca65ae1
- 1mo ago First seen · 188 lines · 100 tokens per session scan A 6cb6c7b206c6
scvi-tools is a skill published in the GitHub repository aipoch/open-science (5,301 stars, last pushed today), licensed Apache-2.0. It adds 100 tokens to every session and 2,860 once invoked, about $0.0004 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 2026-08-30.
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