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 simpygit 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/simpy)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/simpy"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/simpy/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/simpy"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/simpy.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- 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 | $0.00042 | $0.03079 |
| Opus 5 | $0.00021 | $0.01540 |
| Sonnet 5 | $0.00008 | $0.00616 |
| Haiku 4.5 | $0.00004 | $0.00308 |
Grade A, and why
simpy 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 6d 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 — 301 lines — stays where its author put it; the contents beside it link to each section on GitHub.
SimPy
Scope
Use this skill for process-based discrete-event models where active entities yield events and contend for resources: queues, production systems, logistics, networks, service operations, inventory, and other event-driven systems.
SimPy supplies an event scheduler and modeling primitives. It does not choose a scientifically valid conceptual model, input distribution, warm-up, run length, replication count, estimand, or causal interpretation. Treat those as simulation-study methodology, not SimPy API behavior.
Current release and installation
Verified 2026-07-23:
- Latest stable: SimPy 4.1.2, released on PyPI 2026-05-24; source tag
4.1.2points to commitf4381649. - Package metadata requires Python >=3.8 and classifies CPython 3.8-3.14 plus PyPy. SimPy has no runtime dependencies.
- 4.1.2 adds Python 3.13/3.14 support and modern-interpreter test fixes.
- Upstream and this skill are MIT-licensed.
Create a reproducible environment:
uv venv --python 3.13
source .venv/bin/activate
uv pip install "simpy==4.1.2"
python -c "import importlib.metadata; print(importlib.metadata.version('simpy'))"
Do not silently substitute the latest documentation build: it may describe an
unreleased development revision. Use the versioned 4.1.2 links in
references/sources.md.
Model workflow
- Define purpose and estimands. State the decision/question, system boundary, entities, resources, state, outputs, time units, and terminating event or steady-state target.
- Write a conceptual model first. Record assumptions, distributions, routing, priorities, initial conditions, and omitted mechanisms.
- Implement generators. A SimPy process is an event-yielding Python generator.
Register the generator object with
env.process(...). - Bound execution. Give every production run explicit time, entity, event, and
replication caps. Never call
env.run()on a model containing an endless process. - Separate random streams. Use local RNG instances for logically distinct stochastic sources; retain a seed manifest.
- Instrument deliberately. Observe state after the transition of interest, close time-weighted intervals at the horizon, and test that monitoring does not alter event order.
- Verify and validate. Test deterministic edge cases, conservation identities, traces, queue discipline, and analytical benchmarks; compare against system or expert evidence for the stated purpose.
- Run independent replications. Make intervals from replication-level estimates, not correlated entities within one run.
- Report limitations. Include initialization, unfinished entities, run length, seeds/streams, precision, sensitivity, and validation evidence. Never convert simulation association into a causal claim.
What ships with it
15 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/cli-guide.md 7.7 KB
- references/events.md 7.1 KB
- references/monitoring.md 8.1 KB
- references/process-interaction.md 7.5 KB
- references/real-time.md 5.0 KB
- references/resources.md 8.3 KB
- references/simulation-methodology.md 11 KB
- references/sources.md 9.6 KB
- scripts/_common.py 15 KB runs code
- scripts/basic_simulation_template.py 13 KB runs code
- scripts/bounded_queue_scenario.py 3.5 KB runs code
- scripts/event_trace_summary.py 11 KB runs code
- scripts/replication_runner.py 6.1 KB runs code
- scripts/resource_monitor.py 16 KB runs code
- scripts/validate_simulation_config.py 3.6 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.
- 6d ago First seen · 301 lines · 42 tokens per session scan A eb485cdd848d
simpy is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,003 stars, last pushed 2d ago), licensed MIT. It adds 42 tokens to every session and 3,079 once invoked, about $0.0002 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.
notebooks
Author, execute, validate, and convert reproducible marimo or Jupyter notebooks. Use when delivering an analysis notebook with all cells run and figures embedded.