# User Guide

Labrat provides command-line and Python tools designed to improve reproducibility, simplify laboratory management, and support common biomedical research tasks.


# Start here

- [Install Labrat](installation.md) and verify the command-line interface.
- [Query biological databases/APIs](biological-queries.md) such as MyGene, MyVariant, and PubTator 3.
- [Manage projects](project-management.md) from a reusable template and keep a local project list.
- [Organize files and folders](files-and-archives.md).
- [Inspect and translate sequences](sequence-utilities.md) from Python.


# Choose an interface

Use the command-line interface for interactive work and shell pipelines:

``` bash
labrat --help
labrat query --help
```

Use the Python API when a result needs to remain in memory, become part of an analysis, or feed another reproducible step:

``` python
from labrat.query import query_gene

result = query_gene("BMPR2")
print(result.provider)
print(result.retrieved_at)
```


# Query Limitations

Query results depend on live external services and their current database builds. Labrat records retrieval time and provider metadata. Save JSON output to preserve the returned content used in an analysis or report.

File organization commands modify local files. Review the relevant guide and the files in `Downloads` and `Documents` before running them.