Introduction

The pysd2cat circuit analysis tool analyzes flow cytometry data to perform the following tasks:

• Predict Live and Dead cells
• Compute the accuracy of a circuit wrt. a GFP threshold

Quick Start:

Currently, pysd2cat runs on the TACC infrastructure so that it may have fast access to data. It assumes a root directory (containing data files) exists on the host at: /work/projects/SD2E-Community/prod/data/uploads/.

• Clone the repo: https://gitlab.sd2e.org/dbryce/pysd2cat.git
• cd pysd2cat

Two install options are available, with or without test-harness:

Without test-harness installed:

• python setup.py install

With test-harness installed:

• pip install -e . [harness]

To run an example analysis script (test-harness needed), run:

• python src/pysd2cat/analysis/live_dead_analysis.py

Environment Configuration:

You will need to have the following dependencies and logins:

1. pip install transcriptic
2. pip install autoprotocol
3. Get a transcriptic login from Transcriptic (or Strateos). Talk to Josh Nowak.
4. Run transcriptic login once so that it creates the required folders to fetch data.

Code Layout:

The source code is divided into subdirectories, as follows:

• src/pysd2cat/data: routines to acquire data and metadata
• src/pysd2cat/analysis: routines to analyze data
• src/pysd2cat/plot: routines to plot data