How do I install the Yeast Database skill?

Run npx skillmds add vimalinx/yeast-database in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Yeast Database safe to use?

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Which AI agents work with Yeast Database?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Yeast Database free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Yeast Database?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Yeast Database by vimalinx — Agent Skill

Name: Yeast Database
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

yeast_database

Project-specific gateway for /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning. This is a learning project, not a single executable: the real entrypoints are the staged Bash scripts under scripts/, while scripts/pipeline.py provides a compatibility wrapper for --steps and --validate.

Quick Start

Project root: /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning
Primary entrypoint: bash scripts/01_setup_database.sh
Compatibility entrypoint: python scripts/pipeline.py --steps

When To Use This Tool

Downloading and organizing the local yeast reference genome and annotations
Verifying that the learning project's database files and helper tools are ready
Walking through the yeast learning workflow step by step
Running simple gene extraction, sequence analysis, and BLAST exercises inside the project

Common Patterns

# List the available learning steps
cd /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning
python scripts/pipeline.py --steps

# Download the yeast database bundle
cd /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning
bash scripts/01_setup_database.sh

# Verify the setup, then extract a gene
cd /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning
bash scripts/02_verify_install.sh
bash scripts/03_extract_gene.sh ACT1

Recommended Workflow

Enter the local project directory first.
Run the setup script to download the reference genome, annotations, proteins, and BLAST databases.
Validate the installation before doing gene-level or BLAST exercises.
Use the numbered Bash scripts as the primary learning flow, and use pipeline.py only as a compatibility helper for listing/validating steps.

Guardrails

This is explicitly a learning project. The README says the main entrypoints are the staged Bash scripts, not a unified production pipeline.
python scripts/pipeline.py --steps works locally and lists the current teaching steps, but pipeline.py is only a compatibility wrapper.
scripts/01_setup_database.sh downloads data from NCBI/SGD over FTP/HTTP, so network access is required.
samtools and makeblastdb are optional in the setup script: if missing, indexing or BLAST database creation is skipped with warnings.
The old autogenerated skill pointed at ~/bio_studio/projects/yeast_genome_learning/; the actual workspace path is /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning.

---name: yeast-databasedescription: Use when working inside the local `yeast_genome_learning` project to download, validate, and analyze Saccharomyces cerevisiae reference data through its teaching scripts.--- # yeast_database Project-specific gateway for `/home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning`. This is a learning project, not a single executable: the real entrypoints are the staged Bash scripts under `scripts/`, while `scripts/pipeline.py` provides a compatibility wrapper for `--steps` and `--validate`. ## Quick Start - **Project root:** `/home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning` - **Primary entrypoint:** `bash scripts/01_setup_database.sh` - **Compatibility entrypoint:** `python scripts/pipeline.py --steps` ## When To Use This Tool - Downloading and organizing the local yeast reference genome and annotations - Verifying that the learning project's database files and helper tools are ready - Walking through the yeast learning workflow step by step - Running simple gene extraction, sequence analysis, and BLAST exercises inside the project ## Common Patterns ```bash # List the available learning steps cd /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning python scripts/pipeline.py --steps ``` ```bash # Download the yeast database bundle cd /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning bash scripts/01_setup_database.sh ``` ```bash # Verify the setup, then extract a gene cd /home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning bash scripts/02_verify_install.sh bash scripts/03_extract_gene.sh ACT1 ``` ## Recommended Workflow 1. Enter the local project directory first. 2. Run the setup script to download the reference genome, annotations, proteins, and BLAST databases. 3. Validate the installation before doing gene-level or BLAST exercises. 4. Use the numbered Bash scripts as the primary learning flow, and use `pipeline.py` only as a compatibility helper for listing/validating steps. ## Guardrails - This is explicitly a learning project. The README says the main entrypoints are the staged Bash scripts, not a unified production pipeline. - `python scripts/pipeline.py --steps` works locally and lists the current teaching steps, but `pipeline.py` is only a compatibility wrapper. - `scripts/01_setup_database.sh` downloads data from NCBI/SGD over FTP/HTTP, so network access is required. - `samtools` and `makeblastdb` are optional in the setup script: if missing, indexing or BLAST database creation is skipped with warnings. - The old autogenerated skill pointed at `~/bio_studio/projects/yeast_genome_learning/`; the actual workspace path is `/home/vimalinx/Projects/bio_studio/projects/yeast_genome_learning`.

Frequently asked questions