labrat

A basic science lab framework aimed at reproducibility and lab management. This package is in the very early stages of development.

Features

• Easily use math functions to dilute solutions, calculate molarity, etc.
• Backup your documents using the command-line
• Manage lab inventory using a GUI
• Create and manage new projects using the command-line

Install

1. Clone this repository.
2. Change to the downloaded repository’s base directory.
3. pip install .

If you want to develop or contribute to this package, install with pip install -e .

Examples

Dilute a stock concentration

from labrat.math import dilute_stock

# Get the final concentration
dilute_stock(100, 2, **{'vF': 4})

Project Management

Create a new project using the below code. This will create a .labrat file that contains the project information for any project created.

# Create a new project
import os
from labrat.project import ProjectManager

# Initialize the ProjectManager with a username
project_manager = ProjectManager('Dr. Jane Doe')

# Create a new project
project_manager.new_project(
    project_type='computational-biology',
    project_name='KARG Analysis',
    project_path=os.getcwd(),
    description="Analyze the KARG data."
)

Archive a project:

from projectmanager import ProjectManager

project_manager = ProjectManager()
project_path = "/Users/shutchens/Documents/Git-Repos/labrat/karg_analysis"
archive_base_dir = "/Users/shutchens/Archive"

archive_dir = project_manager.archive_project(project_path=project_path, archive_base_dir=archive_base_dir)

Delete a project:

# Path to the project to delete
project_path = "/Users/shutchens/Documents/Git-Repos/labrat/karg_analysis"
archive_base_dir = "/Users/shutchens/Archive"

# Delete the project
archived_path = project_manager.delete_project(project_path, archive_base_dir)

ToDo

• Add a lab inventory app
• Add project report template
• Command-line functionality
• Integrate exmemo

Author

Shaurita Hutchins · @sdhutchins · :email:

Contributing

If you would like to contribute to this package, install the package in development mode, and check out our contributing guidelines.

License

MIT