Worklist Generator

A tool for creating randomized, blocked, high‑power LC–MS worklists

Table of Contents

• Overview
• Installation Options
• Virtual Environment
• Requirements
• Command‑Line Usage
• Glossary
• Cite & Acknowledge

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Overview

The Worklist Generator helps researchers quickly create statistically robust worklists for LC–MS experiments. It supports up to three 16×24 well plates and allows each well to be labeled as an experimental condition or one of several non‑condition types (QC, WetQC, Library, Blank, TrueBlank, or System Validation). The program:

• Randomizes and blocks experimental conditions
• Builds block structures for non‑condition wells (QC/Blank/TrueBlank/WetQC)
• Inserts QC/blank/system‑validation blocks at user‑defined frequencies
• Produces a final, instrument‑ready worklist

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Installation Options

Installation -- github.com

1. Download the latest version from GitHub:
   • https://github.com/RTKlab-BYU/worklist_generation.git
2. Click the green "<> Code" button → Download ZIP.
3. Extract the ZIP using File Explorer (Windows) or Finder (macOS).
4. Open the folder with your preferred IDE or a terminal.

Note: Commands below assume Python 3 is available on your system. Visit https://www.python.org/downloads/ to install python on your computer.

Installation -- Commandline

1. Access your commandline through your preferred program such as Terminal (MacOS), PowerShell (Windows), or VSCode.
2. Enter the following code:

git clone https://github.com/(yourusername)/worklist-generator.git ## enter your github username in place of '(yourusername)'.
cd worklist-generator
pip install -r requirements.txt

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Create and Activate Virtual Environment (optional)

Creating a virtual environment helps to protect your computer.

python3 -m venv .venv
source .venv/bin/activate

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Install Requirements

Run the following after navigating to worklist_git to download the package requirements of the program:

pip install -r requirements.txt

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Command‑Line Usage

1. Generate metadata sheet

python run.py -s 1

• Metadata sheet is found in your Downloads folder.

2. Download the Excel Template

python run.py -s 2 -m <metadata_excel_path>

• Creates a blank template in your Downloads folder.
• If <template_name_optional> is provided, it will be used as the file name.

3. Generate a Worklist from a Completed Template

python run.py -s 3 -w <worklist_excel_path> -o <output_dir>

• <worklist_excel_path> and '<output_dir>' can be copied via your file explorer (e.g., Right‑click → Copy as path). Example:
  • C:\\Users\\myaccount\\Downloads\\mytemplate.xlsx

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Cite & Acknowledge

This README summarizes the Worklist Generator User Guide and the program’s public repository.

• GitHub: https://github.com/RTKlab-BYU/worklist_generation.git

If you use this tool in a publication, please cite your laboratory and/or include a reference to the Worklist Generator repository.