MassDash Installation on Windows 10

This guide will walk you through the installation of MassDash on a Windows 10 machine.

Note

This tutorial was created using a clean installation of Windows 10 using a virtual machine. The virtual machine was created using Oracle VM VirtualBox, with 50Gb of RAM, 8 processors, and 50Gb of storage. The virtual machine was created using the Windows 10 ISO file from Microsoft.

Prerequisites

It is recommended to use Anaconda to manage Python environments and packages. You can download Anaconda from here. You can find documentation for installing Anaconda on windows here.

Installation

  1. Launch the Anaconda Navigator from the start menu.

  2. Launch the Anaconda CMD.exe Prompt from the Anaconda Navigator.

../_images/windows_anaconda_nav_cmd_prompt_launch.png

  1. Create a new environment by running the following command in the Anaconda CMD.exe Prompt:

conda create -n massdash python=3.9 -y
../_images/windows_conda_cmd_prompt_create_env.png

  1. Activate the new environment by running the following command in the Anaconda CMD.exe Prompt:

conda activate massdash
../_images/windows_conda_cmd_activate_env.png

  1. Install MassDash by running the following command in the Anaconda CMD.exe Prompt:

pip install massdash
../_images/windows_conda_cmd_install_massdash.png

Usage

Help

You can get help on how to use MassDash’s GUI by running the following command in the Anaconda CMD.exe Prompt:

massdash gui --help
../_images/windows_conda_cmd_massdash_gui_help.png

Launch MassDash GUI

You can launch MassDash’s GUI by running the following command in the Anaconda CMD.exe Prompt:

massdash gui

A browser window will open with the MassDash GUI. If the browser window does not open, you can navigate to the following URL in your browser using the local url provided in the Anaconda CMD.exe output, by default it should be http://localhost:8501/, unless the port is changed.

Note

MassDash warns you that onnxruntime, torch, and torchmeets are not installed. You can ignore this warning if you do not plan to use the MassDash’s peak picking conformer model.

../_images/windows_conda_cmd_massdash_gui_run.png

Once the browser window opens, you can start using MassDash’s GUI to visualize your mass spectrometry data. For more information on the GUI, please refer to the MassDash GUI Documentation.

../_images/windows_massdash_gui.png ../_images/windows_massdash_gui_example.png