massdash 0.0.8

massdash

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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

or if you use Anaconda for package and environment management, then you can install from bioconda:

conda install bioconda::massdash

Installing from source

Clone the repository:

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

Change into massdash directory:

cd massdash

Install massdash in editable mode:

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.

Citation

Sing, J. C., Charkow, J., AlHigaylan, M., Horecka, I., Xu, L., & Roest, H. L. (2024). MassDash: A Web-based Dashboard for Targeted Mass Spectrometry Visualization (p. 2024.01.15.575772). bioRxiv. https://doi.org/10.1101/2024.01.15.575772