mdadash

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Table of Contents

• About
• Features
• Getting Started
  • Installation
  • Running
  • Accessing Dashboard
• Documentation
• Development
• Copyright
• Acknowledgements

About

mdadash is a browser-based real-time dashboard for monitoring, tracking and analyzing running MD simulations using the streaming interface of MDAnalysis.

The dashboard provides an easy-to-use interface to monitor and control simulation progress. It provides several built-in analyses that can be easily added and customized to analyze running MD simulations via real-time plots. There is support for simple frame-local analyses as well as advanced time-dependent analyses like autocorrelations or lag-time dependent observables. In addition to built-in analyses, the dashboard provides a simple framework for researchers to add their own custom analyses through a Notebook interface directly from within the dashboard and customize it for their own use cases. There is also support to display live 3D visualization of the simulation as it progresses.

Features

• Support for IMDv3 (imd://) as well as file based trajectories

• Multiple built-in analysis widgets

  • See full list in Built-in Analysis Widgets documentation

    

• Customizable dashboard grid layout

• Real-time plots

• Simulation control

  • Connect / Disconnect / Pause / Resume

    

• Custom Code Widget

  • Add custom analysis code

  • See Custom Code Widget documentation

    

• Custom Analysis Widgets

  • Customize built-in widgets

  • Add your own custom analysis widgets

  • See Adding Custom Widgets in documentation

  • Notebook interface

    

• Live 3D visualization

  • Customizable selection

  • Mol * interface

    

• Alerts

  • Notifications when conditions met
  • Ability to pause simulation for further analysis when conditions met

• Batching

  • Support for running widgets in batch mode
  • Support for buffered access and AnalysisBase based classes
  • See Batching in documentation

• Parallelization

  • Support for running widgets in parallel
  • See Parallelization in documentation

• Scalable architecture

  • See Architecture in documentation

Getting Started

Installation

mdadash can be installed in any of the following ways depending on your Python environment:

pip install mdadash

or

uv add mdadash

or

conda install -c conda-forge mdadash

or

mamba install -c conda-forge mdadash

To execute directly from an isolated environment without installing:

uvx mdadash -h

Running

Once the package is installed, it can be run using the mdadash command to start the dashboard server:

mdadash --topology <topology_filename> --trajectory <trajectory_url_or_file>

mdadash supports both streaming and file based trajectories. Here are examples for both cases:

Streaming:

mdadash --topology topology.tpr --trajectory imd://localhost:8889

File based trajectories:

mdadash --topology topology.tpr --trajectory trajectory.xtc

To see a list of all the available options:

mdadash -h

$ mdadash -h
usage: mdadash [-h] --topology TOPOLOGY --trajectory TRAJECTORY [--state-file STATE_FILE] [--clear-alerts]
               [--dashboard-port DASHBOARD_PORT] [--dashboard-host DASHBOARD_HOST] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]

Start the MDA Dashboard server

options:
  -h, --help            show this help message and exit
  --topology TOPOLOGY   Topology filepath (required)
  --trajectory TRAJECTORY
                        Trajectory URL or file (Eg: 'imd://host:port' or trajectory.xtc) (required)
  --state-file STATE_FILE
                        The dashboard state file (default: mdadash.state.json)
  --clear-alerts        Clear alerts if any from dashboard state
  --dashboard-port DASHBOARD_PORT
                        Port to run the dashboard server on (default: 8000)
  --dashboard-host DASHBOARD_HOST
                        Host address to bind dashboard server to (default: 127.0.0.1)
  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set the logging level (default: INFO)
  -v, --version         Show the dashboard version and exit

Accessing Dashboard

The dashboard can be accessed by navigating to http://127.0.0.1:8000 using any browser.

Note:

Both the dashboard host and post can be customized using the mdadash command line options.

Setting --dashboard-host 0.0.0.0 will make the dashboard server accessible from any machine over the network.

Documentation

Documentation for mdadash is available at: https://mdadash.readthedocs.io/

Development

mdadash is bound by a Code of Conduct.

Developer instructions for this project can be found here.

Copyright

The mdadash source code is hosted at https://github.com/MDAnalysis/mdadash and is available under the MIT License (see the file LICENSE).

Copyright (c) 2026, MDAnalysis

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using mdadash in published work.