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A basic science lab framework aimed at reproducibility and lab management.

License: MIT License

Python 100.00%

genetics science laboratory laboratory-automation psychiatry molecular-biology lab gui labrat python

labrat's Introduction

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

Clone this repository.
Change to the downloaded repository's base directory.
pip install .

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

This package is compatible with python 3.4 and up.

Examples

Dilute a stock concentration

from labrat.math import dilute_stock

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

Create a new computational biology project

from labrat.project import ProjectManager
projectmanager = ProjectManager('Dr. Jane Doe')
projectmanager.new_project(project_type='computational-biology',
                          project_name='KARG Analysis',
                          project_path=os.getcwd())

ToDo

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

Author

Shaurita Hutchins · @sdhutchins · 📧

Contributing

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

License

labrat's People

Contributors

Stargazers

Watchers

Forkers

davlu andytempel karillith wizofe hatoris

labrat's Issues

Create cli template for given functions

Use python fire to create a cli mockup.

Check out using a fire cli and the python fire guide.

Add fire as a dependency to setup.py and requirements.txt
Create mockup in dev-master branch

Decide on a gui framework

I think Flask React would be a great way to implement a newer technology into this.

Calling all Scientists, Researchers, Students! Add relevant lab related math functions!

I'm looking to add more useful lab related math functions to this package. Check here for what I currently have which is not much.

If you have any other ideas about the package, please chime in on this issue.

Create alpha and beta versioning phases

Create alpha and beta versioning phases for the app.

So far... I think 0.1a is the way to go.

Integrate with readthedocs and sphinx

Add additional project templates

Currently, only the cookiecutter for a computational biology project exists.

Decide on other types of project templates.

PCR/Genotyping
Cell culture (transfection experiments? stable cell lines)

Integrate exmemo

Use existing framework such as exmemo to implement features for notebook creation.

Integrate with a lab/science glossary

Allow users to have access to descriptions of basic techniques via the command line.

Calling all Scientists, Researchers, Students! Add a new feature to labrat!

You may address any of the items below or suggest/add a new feature.

Add a lab inventory app/gui
Add project report template
Add a calculator gui
Command line functionality

Check out the contributing docs for more details.

Add PCR and qPCR related functions

Ensure that PCR and qPCR are accounted for.

Experiment preparation
Experiment analysis (and maybe data visualization)

Add docstrings

A docstrings that fit with google python style guide.

Create a lab report template

Allow users to create lab reports using their python functions.

This can be something that uses markdown or plain text and includes python.

Decide on the scope of this project

Is this a comprehensive framework?

Limit this to project management and experimental reproducibility?

Limit this to experiment reproducibility and ease of use?

Integrate with other useful apis

entrez, mygene, ncbi, etc.

Using pint for math function

Should integrated pint for function in your math module.

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