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 pacsomaticgit 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/pacsomatic)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/pacsomatic"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/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/synthetic-sciences/openscience/pacsomatic"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/pacsomatic.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 | $0.00103 | $0.01280 |
| Opus 5.5 | $0.00041 | $0.00512 |
| Sonnet 5.5 | $0.00021 | $0.00256 |
| Haiku 4.5 | $0.00010 | $0.00128 |
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 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
94% identical to pacsomatic — 207 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 — 158 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.
- 1mo ago Changed · +5 lines c83ee6fb5b5b
- 1mo ago First seen · 153 lines · 103 tokens per session scan A b1f2307042d1
pacsomatic is a skill published in the GitHub repository synthetic-sciences/openscience (4,025 stars, last pushed today), licensed Apache-2.0. It adds 103 tokens to every session and 1,280 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 94% identical to pacsomatic, differing in 207 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.