diff --git a/joss_paper/paper.md b/joss_paper/paper.md index 3272cc9..bf1ef43 100644 --- a/joss_paper/paper.md +++ b/joss_paper/paper.md @@ -51,6 +51,8 @@ Molecular dynamics (MD) simulations provide a microscope into the behavior of atomic-scale environments otherwise prohibitively difficult to observe. However, the resulting trajectory data are too often siloed in a single institutions' HPC environment, rendering it unusable by the broader scientific community. +Additionally, it is increasingly common for trajectory data to be entirely +stored in a cloud storage provider, rather than a traditional on-premise storage site. *Zarrtraj* enables these trajectories to be read directly from cloud storage providers like AWS, Google Cloud, and Microsoft Azure into MDAnalysis, a popular Python package for analyzing trajectory data, providing a method to open up access to @@ -179,12 +181,12 @@ with fsspec.open("gcs://zarrtraj-test-data/YiiP_system.pdb", "r") as top: u = mda.Universe(top, "gcs://zarrtraj-test-data/yiip.zarrmd", topology_format="PDB") - for ts in u.trajectory[100::20]: - print(ts) + for timestep in u.trajectory[100::20]: + print(timestep) ``` Inside the loop over trajectory frames we print information for the current -frame `ts` although in principle, any kind of analysis code can run here and +frame `timestep` although in principle, any kind of analysis code can run here and process the coordinates available in `u.atoms.positions`. The `Universe` object can be used as if the underlying trajectory file were a @@ -217,7 +219,7 @@ or any script or package that uses MDAnalysis for file I/O. # Acknowledgements We thank Dr. Jenna Swarthout Goddard for supporting the GSoC program at MDAnalysis and -Martin Durant, author of Kerchunk, for helping refine and merge features in his upstream code base +Dr. Martin Durant, author of Kerchunk, for helping refine and merge features in his upstream code base necessary for this project. LW was a participant in the Google Summer of Code 2024 program. Some work on *Zarrtraj* was supported by the National Science Foundation under grant number 2311372.