AnalysisTool-for-Bioreactor

Introduction

Welcome to the AnalysisTool-for-Bioreactor console application! This guide will walk you through the setup and usage of the tool.

Prerequisites

1. Update your username: Replace <currentUser> with your actual username in the steps below Here’s the corrected sentence: (Example for saving the repo on Desktop).
2. Install .NET 8.0: If not installed, download it from here.
3. Prepare your data: Copy and paste your data table into the InsertTableHere folder (/AnalysisTool-for-bioreactor/InsertTableHere).
4. Check the output: After analysis, find the results in the Output folder (including data analysis tables and plot HTML files).

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Step-by-Step Guide (New Version)

Windows:

1. Open RunAnalysisTool_Windows.bat by double-click or using right-click and open with PowerShell.

MacOS:

1. Open Terminal and run:

   xattr -d com.apple.quarantine /path/to/Analysis-Tool-For-Bioreactor/RunAnalysisTool_MacOS.app

2. Open RunAnalysisTool_MacOS.app by double-clicking it. (Note: If blocked due to an unidentified developer, go to Settings > Privacy & Security, scroll down, and press “Allow Anyway.”)

Alternative MacOS:

1. Open Terminal, navigate to the folder:

   cd /Users/<currentUser>/Desktop/AnalysisTool-for-bioreactor/Analysis_Tool_dependencies

2. Run the application:

   pwsh ./run_Analysis_Tool.ps1

(You may need to install PowerShell. If not installed, download it from here

Step-by-Step Guide (Old Version for Windows or MacOS):

1. Open the console and navigate to the app data path.

   cd /Users/<currentUser>/Desktop/AnalysisTool-for-bioreactor/Analysis_Tool_dependencies/Analysis/src/App

2. Start the application:

   dotnet run
   

Input Format

Provide the input in the following format:

202310_TR16_HLexperiment_RawData_Venny_Simon 0.44 0.36 3

or

202310_TR16_HLexperiment_RawData_Venny_Simon 0.44 0.36 all

Parameters:

• Filename: The .txt data table must contain all 8 columns (Light, OD, and pump data).
• Upper OD Threshold: A number with a decimal point, e.g., 3.0.
• Lower OD Threshold: A number with a decimal point, e.g., 3.0.
• Cylinder: Choose a number between 1 and 8, or use all.

Troubleshooting

If the application fails and you cannot identify the issue, please contact [email protected].