Skills

A skill is a package of structured files that teaches an AI coding agent how to work with a specific tool or framework. The skill below was generated by Great Docs from this project’s documentation. Install it in your agent and it will be able to run commands, edit configuration, write content, and troubleshoot problems without step-by-step guidance from you.

Any agent — install with npx:

npx skills add https://www.shauritahutchins.com/labrat/

Codex / OpenCode

Tell the agent:
Fetch the skill file at https://www.shauritahutchins.com/labrat/skill.md and follow the instructions.

Manual — download the skill file:

curl -O https://www.shauritahutchins.com/labrat/skill.md

Or browse the SKILL.md file.

SKILL.md

---
name: pylabrat
description: >
  A Python framework designed to improve reproducibility, simplify laboratory management, and support common biomedical research tasks. Use when writing Python code that uses the labrat package.
license: MIT
compatibility: Requires Python >=3.10.
---

# labrat

A Python framework designed to improve reproducibility, simplify laboratory management, and support common biomedical research tasks.

## Installation

```bash
pip install pylabrat
```

## API overview

### Query models and clients

Shared results and clients for external biological resources.

- `query.QueryResult`
- `query.QueryError`
- `query.PubTatorClient`

### Biological queries

Gene, variant, and biomedical literature queries.

- `query.query_gene`
- `query.query_variant`
- `query.query_literature`

### Project and file management

Classes for projects, archives, and scientific files.

- `project.ProjectManager`
- `filemanager.Archiver`
- `filemanager.FileOrganizer`

### ProjectManager methods

- `project.ProjectManager.new_project`
- `project.ProjectManager.list_projects`
- `project.ProjectManager.update_project`
- `project.ProjectManager.list_project_files`
- `project.ProjectManager.archive_project`
- `project.ProjectManager.add_template`
- `project.ProjectManager.delete_project`

### FileOrganizer methods

- `filemanager.FileOrganizer.move_file`
- `filemanager.FileOrganizer.organize_by_year`
- `filemanager.FileOrganizer.organize_documents`
- `filemanager.FileOrganizer.organize_archives`
- `filemanager.FileOrganizer.organize_files`
- `filemanager.FileOrganizer.move_specific_files`
- `filemanager.FileOrganizer.organize_science_files`
- `filemanager.FileOrganizer.organize_all`

### Genetics

DNA and protein sequence utilities.

- `genetics.atgc_content`
- `genetics.complementary_dna`
- `genetics.dna2aminoacid`

### Laboratory math

Common concentration and optical calculations.

- `math.calculate_molarity`
- `math.dilute_stock`
- `math.mass_recorder`
- `math.refractive_index_prism`
- `math.transmittance_to_absorbance`

## Resources

- [Full documentation](https://www.shauritahutchins.com/labrat/)
- [llms.txt](llms.txt) — Indexed API reference for LLMs
- [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs