singjust/massdash repository overview

MassDash is a powerful platform designed for researchers and analysts in the field of mass spectrometry. By providing a centralized web-based dashboard, MassDash facilitates data analysis and experiment design by enabling users to visualize chromatograms, test algorithms, and optimize parameters. This tool offers a flexible environment for mass spectrometry research, with notable specailty in handling Data-Independent Acquisition (DIA) data.

⁠Installation

Recommended: Install the latest stable version of MassDash from the Python Package Index (PyPI):

pip install massdash --upgrade

git clone https://github.com/Roestlab/massdash.git

cd massdash

pip install -e .

⁠Quick start

Launch MassDash by typing the following command in your terminal:

massdash gui

⁠Features

MassDash empowers researchers to streamline mass spectrometry workflows, experiment with data analysis algorithms, and optimize parameters to enhance research accuracy and efficiency. Below are some of MassDash's notable features:

• Chromatogram visualization: Easily view and analyze chromatograms for an in-depth examination of mass spectrometry data.

• Algorithm testing: Develop and fine-tune custom algorithms by interfacing with MassDash's various data analysis algorithms and workflows.

• Parameter optimization: Ensure optimal results for your experiment by optimizing parameters for data analysis workflows, such as OpenSwathWorkflow.

• User-friendly dashboard: MassDash's dashboard is designed with users in mind, facilitating research productivity in both beginners and experts in the field.

• Data exploration: Explore mass spectrometry data with our suite of tools and gain insights to make informed research decisions.

• Customization: Flexibly tailor data analysis parameters and results for specific research needs.

• Rapid prototyping: Save time and resource when developing mass spectrometry workflows by quickly prototyping and testing research ideas.

• Data integration: Seamlessly import, process, and export data to facilitate data sharing and collaboration.

⁠Launching MassDash from a remote machine

SSH into a remote machine and install massdash; it's highly recommended to install massdash in a Python virtual environment to contain project-specific dependencies:

ssh your_user_name@remote_ip_address

pip install massdash

Launch MassDash:

massdash gui

Two URLs with an IP address and port number will appear in the terminal after launching MassDash; for example:

  Network URL: http://192.168.142.176:8501
  External URL: http://142.150.84.40:8501

Enter the following command in a local machine's terminal, replacing "----" with the URL port number (e.g., 8501):

ssh -fNL ----:localhost:---- your_user_name@remote_ip_address

You can now view MassDash on the local machine's browser by clicking on either of the provided URLs.

⁠Docker

MassDash is also available on Docker.

Pull the latest stable version of MassDash from DockerHub:

docker pull singjust/massdash:latest

Spin up the MassDash Docker container:

docker run -p 8501:8501 singjust/massdash:latest

Note: The MassDash Docker image binds to port 8501 when running MassDash locally.

⁠Contribute

• Issues Tracker⁠
• Source Code⁠

⁠Support

If you are having issues or would like to propose a new feature, please use the issues tracker⁠.

⁠License

This project is licensed under the BSD 3-Clause license.