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 GPTomics/bioSkills --skill focal-amplification-ecdnagit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/focal-amplification-ecdna)<a href="https://agentmods.dev/skills/gptomics/bioskills/focal-amplification-ecdna"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/focal-amplification-ecdna/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/gptomics/bioskills/focal-amplification-ecdna"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/focal-amplification-ecdna.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 | $0.00149 | $0.02605 |
| Opus 5 | $0.00075 | $0.01303 |
| Sonnet 5 | $0.00030 | $0.00521 |
| Haiku 4.5 | $0.00015 | $0.00261 |
Grade A, and why
bio-copy-number-focal-amplification-ecdna 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 7d 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:
- bio-copy-number-focal-amplification-ecdna — 98% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 173 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: AmpliconSuite-pipeline 1.3+, AmpliconArchitect 1.3+, AmpliconClassifier 1.2+, CNVkit 0.9.10+, Python 3.10+, samtools 1.19+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
AmpliconSuite-pipeline.py --help,amplicon_classifier.py --help - AmpliconArchitect needs a
$AA_DATA_REPOreference download and a Mosek license (free for academic use); confirm both are configured before running
Verify the reference build — AmpliconArchitect was historically hg19-centric; GRCh38 support and data repos exist but the build must be set explicitly and consistently.
Focal Amplification and ecDNA
"This oncogene is amplified — but how, structurally" -> A depth caller reports "high focal amplification" and stops. The biology depends entirely on the architecture: extrachromosomal DNA (ecDNA) behaves utterly differently from a chromosomal homogeneously staining region. Resolving architecture needs the breakpoint graph, not depth.
- CLI:
AmpliconSuite-pipeline.py(end-to-end),AmpliconArchitect(graph reconstruction),AmpliconClassifier(architecture call) - Input: WGS BAM plus copy-number seeds (high-CN focal regions)
Why Architecture Matters — Four Amplicon Classes
| Class | Structure | Behavior | Why it matters |
|---|---|---|---|
| ecDNA | Circular, episomal, no centromere | Hundreds of copies; unequal mitotic segregation; rapid CN adaptation | Drives oncogene overexpression, intratumor heterogeneity, therapy resistance; ~14% of cancers |
| BFB | Chromosomal, fold-back inversions | Stepwise CN gradient toward telomere | Distinct breakpoint signature; bounded amplification |
| HSR | Linear, integrated chromosomally | Stable inheritance | Chromosomal — segregates evenly, unlike ecDNA |
| Linear/simple | Tandem or simple amplification | Modest copy gain | Often passenger-scale; lowest oncogenic concern |
ecDNA is the highest-stakes call: because it lacks a centromere it segregates unequally, so copy number can surge under selection — a structural basis for resistance. Depth alone cannot distinguish ecDNA from an HSR; both look like a high-amplitude focal gain.
What ships with it
2 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.
- 7d ago First seen · 173 lines · 149 tokens per session scan A 593ef01e8c2a
bio-copy-number-focal-amplification-ecdna is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 149 tokens to every session and 2,605 once invoked, about $0.0007 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.
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