Lawson

Bioinformatic Software developer.

Zarrtraj: Cloud Streaming MD Trajectories into MDAnalysis

zarrtraj is a Python package for reading and writing H5MD trajectory data using the Zarr package which allows streaming trajectories from cloud storage like AWS S3. zarr also allows easy data compression & filtering and comes with some built-in cacheing mechanisms.

zarrtraj allows researchers to make their trajectories publicly available via a simple S3 URL so that anyone with an internet connection can analyze their data in MDAnalysis just by doing this:

u = mda.Universe("topology.pdb", "s3://fake-lab/trajectory.h5md")

Zarrtraj 0.2.0 is out! Check it out on PyPI.

IMDReader: Livestreaming MD Simulations into MDAnalysis

IMD is a simple binary tcp protocol for streaming trajectory data from a live molecular dynamics simulation server (i.e. GROMACS) to a client and allowing the client to input forces back into the simulation. The IMDReader is currently in the early prototyping phase. I’m excited to take this project further in the Fall semester!