zarrtraj

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Zarrtraj is an MDAnalysis MDAKit that provides the ability to read and write H5MD-formatted trajectory data in MDAnalysis using Zarr. Zarrtraj can read trajectories locally and from AWS S3, Google Cloud Buckets, and Azure Blob Storage & DataLakes. It can read both H5MD-formatted files stored in hdf5 (.h5md files) and H5MD-formatted files stored in Zarr (.zarrmd files).

Zarrtraj is installable via both pip and conda forge:

pip install zarrtraj

conda install -c conda-forge zarrtraj

For more information on installation and usage, see the zarrtraj documentation

Zarrtraj is bound by a Code of Conduct.

Copyright

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

Copyright (c) 2024, Lawson Woods

Citation

If you use Zarrtraj in published work, please cite:

Lawson Woods, Hugo MacDermott-Opeskin, Edis Jakupovic, Yuxuan Zhuang, Richard J Gowers, and Oliver Beckstein. (2026). Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services. Journal of Open Source Software, 11(121), 7943, https://doi.org/10.21105/joss.07943

@article{Woods2026zarrtraj,
  author = {Woods, Lawson and MacDermott-Opeskin, Hugo and Jakupovic, Edis and Zhuang, Yuxuan and Gowers, Richard J and Beckstein, Oliver},
  title = {Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services},
  journal = {Journal of Open Source Software},
  year = {2026},
  volume = {11},
  number = {121},
  pages = {7943},
  doi = {10.21105/joss.07943},
  url = {https://doi.org/10.21105/joss.07943}
}

Acknowledgements

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