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 AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cosmicgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-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/alterlab-ieu/alterlab-academic-skills/alterlab-cosmic)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cosmic"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cosmic/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/alterlab-ieu/alterlab-academic-skills/alterlab-cosmic"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-cosmic.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- 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 | $0.00117 | $0.03566 |
| Opus 5.5 | $0.00047 | $0.01426 |
| Sonnet 5.5 | $0.00023 | $0.00713 |
| Haiku 4.5 | $0.00012 | $0.00357 |
Grade A, and why
alterlab-cosmic scanned grade A with 1 finding 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) How it starts
The opening of the file, as written. The whole thing — 303 lines — stays where its author put it; the contents beside it link to each section on GitHub.
COSMIC Database
Overview
COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer. Access COSMIC's extensive collection of cancer genomics data, including millions of mutations across thousands of cancer types, curated gene lists, mutational signatures, and clinical annotations programmatically.
When to Use This Skill
This skill should be used when:
- Downloading cancer mutation data from COSMIC
- Accessing the Cancer Gene Census for curated cancer gene lists
- Retrieving mutational signature profiles
- Querying structural variants, copy number alterations, or gene fusions
- Analyzing drug resistance mutations
- Working with cancer cell line genomics data
- Integrating cancer mutation data into bioinformatics pipelines
- Researching specific genes or mutations in cancer contexts
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| Germline variant pathogenicity (ACMG/AMP, ClinVar stars) | alterlab-clinvar |
| Mutation frequency / OncoPrint / survival in TCGA or MSK cohorts via a keyless API | alterlab-cbioportal |
| CRISPR/RNAi gene dependency in cancer cell lines | alterlab-depmap |
| Population allele frequencies in non-cancer cohorts | alterlab-gnomad |
Prerequisites
Account Registration
COSMIC requires authentication for data downloads:
- Academic users: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register
- Commercial users: A COSMIC commercial licence is required for commercial R&D, products/services, and patient services or clinical reporting — see https://www.cosmickb.org/licensing
Python Requirements
uv pip install requests pandas
# pysam is only needed if you read the VCF-format downloads
uv pip install pysam
Quick Start
COSMIC's current download service delivers each product as a .tar archive (the
gzipped TSV or VCF plus a README describing every column) at an explicit release path,
e.g. grch38/cosmic/v104/Cosmic_GenomeScreensMutant_Tsv_v104_GRCh38.tar. Scripted
downloads are a two-step call: GET https://cancer.sanger.ac.uk/api/mono/products/v1/downloads/scripted?path=<archive path>&bucket=downloads
with HTTP Basic auth (email:password) returns JSON with a signed url, which you then
fetch without auth. The legacy /cosmic/file_download/... endpoint and legacy names such
as CosmicMutantExport.tsv.gz or cancer_gene_census.csv no longer work for scripts —
the old endpoint now redirects to the login page.
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 · +41 lines 08d7ed5ab186
- 1mo ago First seen · 262 lines · 117 tokens per session scan A 602077bd350a
alterlab-cosmic is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 2d ago), licensed MIT. It adds 117 tokens to every session and 3,566 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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