QBiC × BDS Agent Skills Collection (University of Tübingen)

This repository is a curated collection of self-made, Agent Skills--compliant skills developed at the University of Tübingen as a joint effort of the Quantitative Biology Center (QBiC) and the Chair for Biomedical Data Science (BDS).

The primary purpose of this repository is to provide reusable, versioned skills that can be embedded into other Git projects (e.g., agent projects, automation repositories, internal tooling) while keeping validation and maintenance centralized.

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Scope

• A collection of skills stored under ./skills/
• Skills intended to be fully agentskills.io compliant
• Continuous validation via GitHub CI using sklint in strict mode
• Optional agent governance via AGENTS.md (see section below)

This repository is a skills library, not a full agent project.

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Repository Structure

.
├── skills/
│   ├── <skill-name>/
│   │   ├── SKILL.md
│   │   └── ...
├── .github/workflows/
├── AGENTS.md
└── README.md

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Validation (CI)

This repository runs sklint in CI to ensure all skills conform to the Agent Skills specification. sklint is a Go CLI purpose-built for this — it is preferred over the reference implementation (skills-ref) bundled with the agentskills.io repository, which is intended for demonstration purposes only and is not suitable for production CI use.

Typical CI logic:

• Iterate over directories in skills/*
• Run sklint --strict <skill-dir>

For installation instructions and full usage documentation, refer to the sklint repository.

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Recommended Integration into Other Git Projects

Option A: Git Submodule (Recommended)

git submodule add https://github.com/qbicsoftware/agent-skills vendor/tue-skills
git submodule update --init --recursive

Reference skills from:

vendor/tue-skills/skills/<skill-name>

Update later:

git submodule update --remote --merge

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Option B: Git Subtree

git subtree add --prefix vendor/tue-skills https://github.com/qbicsoftware/agent-skills main --squash

Update:

git subtree pull --prefix vendor/tue-skills https://github.com/qbicsoftware/agent-skills main --squash

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Option C: Manual Clone

git clone https://github.com/qbicsoftware/agent-skills

Copy or sync the skills/ directory as needed.

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Using the Skills

Depending on your tooling, you may:

• Point your agent tooling to the skills/ directory
• Symlink selected skills into a local skills folder

Example:

mkdir -p .agents/skills
ln -s ../../vendor/tue-skills/skills/<skill-name> .agents/skills/<skill-name>

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About AGENTS.md and How to Disable It

This repository contains an AGENTS.md to guide agents working inside this repository.

When vendoring this repo (submodule/subtree), you may not want these instructions to apply to your project.

Options to Avoid Inheriting AGENTS.md

1. Run agents from your project root (your own AGENTS.md takes precedence).
2. Place the submodule in a directory like vendor/ or third_party/ and exclude it from agent scanning.
3. Override with your own root-level AGENTS.md.
4. If supported by your tooling, explicitly disable agent instruction scanning for the vendored path.

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Contributing

• Add new skills under skills/<skill-name>/
• Ensure Agent Skills compliance
• Run sklint --strict locally
• CI must pass before merging

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Maintainers

Maintained as a joint effort of:

• Quantitative Biology Center (QBiC), University of Tübingen
• Chair for Biomedical Data Science (BDS), University of Tübingen

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Skills

linear-thinking

Description

Enforce clear, step-by-step, cause→effect reasoning and a single ordered plan. Use for tasks that benefit from structured analysis (requirements, debugging, implementation planning, checklists).

License

AGPL-3.0-only

Metadata

• author: Sven Fillinger
• version: 1.0

License

This repository is lincensed under the AGPL-3.0 license