This package has moved to https://github.com/biocircuits/murraylab_tools and is no longer actively maintained here.

Tools for Common Murray Lab Protocols

Code for common tasks in the Murray lab. Supports Python >=3.6 only.

Install with the following (probably requires sudo): pip install git+https://github.com/biocircuits/murraylab_tools.git@master

To update, run (also with superuser privilege): pip install --upgrade --no-deps git+https://github.com/biocircuits/murraylab_tools.git@master

Currently includes the following subpackages:

utilities: Simple Quality-Of-Life Improvement Tools

• A code block that will automatically text or email you when your code is done running.

echo: Echo Setup for TX-TL Experiments (and others)

Code to produce Echo source plate setup instructions and picklists for one of the following cases:

• A TX-TL experiment with a TX-TL setup spreadsheet.
• Programmatically-constructed TX-TL experiments, including easy 2D dilution series setup plus arbitrary additions.
• Fully general well contents, as defined by a spreadsheet of source materials and a spreadsheet listing what goes in each.

For details, see the "Echo Setup Usage Examples" ipython notebook under "examples".

biotek: Tidying and Analysis of Biotek Plate Reader Data

Code for converting raw excel/CSV data from a Biotek plate reader into tidy format, plus a class to make plotting Biotek data traces quick and easy (BiotekCellPlotter).

Also contains convenience functions for analysis of Biotek timecourse data:

• Fluorescence calibration against lab data (TX-TL data only)
• Background subtraction
• Endpoint averaging
• Data smoothing (spline fit or moving average)
• Smoothed derivative calculation
• OD normalization
• Growth curve summarazation with logistic curve fits

For details, see the "Biotek Analysis Usage Examples" ipython notebook under "examples".