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 pacsomaticgit 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/pacsomatic)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/pacsomatic"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/pacsomatic/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/pacsomatic"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/pacsomatic.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 | $0.00103 | $0.01212 |
| Opus 5 | $0.00051 | $0.00606 |
| Sonnet 5 | $0.00021 | $0.00242 |
| Haiku 4.5 | $0.00010 | $0.00121 |
Grade A, and why
pacsomatic 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 9d 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
4 near-identical copies found in the catalogue:
- pacsomatic — 100% identical, 3 lines differ
- pacsomatic — 100% identical, 4 lines differ
- pacsomatic — 100% identical, 3 lines differ
- pacsomatic — 100% identical, 8 lines differ
How it starts
The opening of the file, as written. The whole thing — 151 lines — stays where its author put it; the contents beside it link to each section on GitHub.
pacsomatic
Overview
This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint that handles validation, artifact generation, and optional execution.
Primary entrypoint:
scripts/run_pacsomatic.py
The helper script:
- validates required identifiers, files, reference mode, and runtime prerequisites
- writes a pacsomatic-compatible samplesheet (
patient,sample,status,bam,pbi) - generates a params YAML and launch script for reproducible reruns
- supports dry-run validation and run/submit execution paths
Use this skill as the default path for pacsomatic operations. Do not bypass it with manually assembled nextflow run nf-core/pacsomatic commands unless the user explicitly asks for manual command construction.
When to Use This Skill
Invoke this skill when the user asks to:
- run matched tumor-normal analysis from BAM files
- generate or fix pacsomatic samplesheet and launch artifacts
- execute locally or submit to schedulers (LSF/Slurm/PBS/SGE)
- perform dry-run validation before execution
- troubleshoot launch failures or summarize run outputs
Do not use this skill for:
- deep biological interpretation beyond run-level sanity checks
- editing pipeline internals unless explicitly requested
Typical trigger phrases:
- "run nf-core/pacsomatic for this tumor-normal pair"
- "prepare pacsomatic samplesheet and launch script"
- "do a dry run first and tell me what is missing"
- "submit pacsomatic to slurm/lsf and return the job id"
- "why did pacsomatic submission fail"
Routing and Execution Rules
- Always collect required run inputs first.
- Always route through
scripts/run_pacsomatic.pyfor validation and artifact generation. - Default to
--dry-runwhen the user asks for checks/validation only. - Use
--runonly when the user asks to execute/submit. - For scheduler modes, include executor-specific resource arguments and return detected job ID when available.
- If execution fails, report first failure point and next triage target (
.nextflow.log,pipeline_info, failing task logs).
What ships with it
6 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.
- 9d ago First seen · 151 lines · 103 tokens per session scan A 7c46a2683bf4
pacsomatic is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed today), licensed MIT. It adds 103 tokens to every session and 1,212 once invoked, about $0.0005 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…
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.
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.
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.