Borrowing it
Nothing to install: this file belongs to bigbio/sdrf-skills. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/bigbio/sdrf-skills/main/GEMINI.mdgit clone --depth 1 https://github.com/bigbio/sdrf-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/instructions/bigbio/sdrf-skills/gemini-md)<a href="https://agentmods.dev/instructions/bigbio/sdrf-skills/gemini-md"><img src="https://agentmods.dev/badge/instructions/bigbio/sdrf-skills/gemini-md/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/instructions/bigbio/sdrf-skills/gemini-md"><img src="https://agentmods.dev/badge/instructions/bigbio/sdrf-skills/gemini-md.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 | $0.01240 | $0.01240 |
| Opus 5.5 | $0.00496 | $0.00496 |
| Sonnet 5.5 | $0.00248 | $0.00248 |
| Haiku 4.5 | $0.00124 | $0.00124 |
Grade A, and why
sdrf-skills GEMINI.md 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 yesterday.
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 — 72 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sdrf-skills — SDRF Annotation Skills
Structured workflows for expert-level SDRF (Sample and Data Relationship Format) annotation in proteomics.
Available Workflows
The skills/ directory contains 20 workflow files (SKILL.md) that encode community
annotation expertise. When working with SDRF files, consult the relevant skill:
- Annotation:
skills/sdrf-annotate/SKILL.md— create an SDRF from a PXD and always have it independently reviewed; review an existing .sdrf.tsv; or plan. The only entry point for annotation and review - Planning:
skills/sdrf-annotate/SKILL.md— pre-annotation metadata strategy - Adversarial review:
skills/sdrf-adversarial-review/SKILL.md— isolated evidence-first review with hash-bound approval - Contribute:
skills/sdrf-contribute/SKILL.md— PR to community repository - Campaign:
skills/sdrf-campaign/SKILL.md— screen a class of studies against your criteria, then loop annotate over the included ones
Specification Data
The SDRF specification lives in the spec/ git submodule:
- Column definitions:
spec/sdrf-proteomics/TERMS.tsv— read this for column names, ontology mappings, allowed values - Template manifest:
spec/sdrf-proteomics/sdrf-templates/templates.yaml— read this for template inventory - Individual templates:
spec/sdrf-proteomics/sdrf-templates/{name}/{version}/{name}.yaml
Skills reference these files at runtime. Never hardcode specification data.
Bundled tools: contract and build
Install the helpers once: pip install -e <sdrf-skills checkout> (brings sdrf-pipelines), then sdrf-tools doctor.
Set SDRF_SKILLS_ROOT to the sdrf-skills checkout: the skills resolve spec/, tools/ and data/
against it (Claude Code sets CLAUDE_PLUGIN_ROOT instead).
Two deterministic helpers keep annotation short and structurally valid. Run them as sdrf-tools ...:
sdrf-tools contract -t ms-proteomics [-t human ...]— prints the column contract of the template union: every column in order, required/optional/multiple, value form, permitted reserved words and the ontologies to search. Read this instead ofTERMS.tsvand the template YAMLs.sdrf-tools build --samples samples.tsv --technical technical.tsv --files files.json -t ms-proteomics [-t ...] -o output.sdrf.tsv— expands a sample table (one row per source and replicate;files= the fractions of one injection;label=label free sampleor one channel) plus a technical table (run-levelcomment[...]values,|between multiple values) into the SDRF: fractions, technical replicates, channel rows, repeated columns and column order are decided by code. It refuses, and writes nothing, on a file outsidefiles.json, a file claimed twice, two rows sharing a (source, biological replicate, technical replicate, fraction) coordinate, or an incomplete channel map — it never fills a channel in.
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.
- yesterday Changed · +4 lines · +77 tokens per session e57307aee747
- 1mo ago Changed · +17 lines · +176 tokens per session 376f7d962804
- 1mo ago First seen · 51 lines · 987 tokens per session scan A 98ea3054249f
sdrf-skills GEMINI.md is an instructions file published in the GitHub repository bigbio/sdrf-skills (19 stars, last pushed yesterday), licensed MIT. It adds 1,240 tokens to every session, about $0.0050 per session on Opus 5.5. 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 2026-08-30.
Other instructions, from other repositories
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AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
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AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
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Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
vscode model-prompts.instructions.md
Model-specific prompt authoring and registry guidelines.