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Update fig 2 link in paper #89

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ljwoods2 merged 1 commit into from
Oct 26, 2025
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Update fig 2 link in paper #89

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2 changes: 1 addition & 1 deletion joss_paper/paper.md
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Expand Up @@ -147,7 +147,7 @@ writing parallelized algorithms can offset this loss of speed as in \autoref{fig

![Benchmarks performed on a machine with 2 Intel Xeon 2.00GHz CPUs, 32GB of RAM, and an SSD configured with RAID 0. The trajectory used for benchmarking was the YiiP trajectory from MDAnalysisData [@YiiP:2019], a 9000-frame (90ns), 111,815 particle simulation of a membrane-protein system. The original 3.47GB XTC trajectory was converted into an uncompressed 11.3GB H5MD trajectory and an uncompressed 11.3GB ZarrMD trajectory using the MDAnalysis `H5MDWriter` and *Zarrtraj* `ZarrMD` writers, respectively. XTC trajectory read using the MDAnalysis `XTCReader` for comparison. \label{fig:benchmark}](benchmark.png)

![RMSD benchmarks performed on the same machine as \autoref{fig:benchmark}. YiiP trajectory aligned to first frame as reference using `MDAnalysis.analysis.align.AlignTraj` and converted to compressed, quantized H5MD (7.8GB) and ZarrMD (4.9GB) trajectories. RMSD performed using development branch of MDAnalysis (2.8.0dev) with "serial" and "dask" backends. See [this notebook](https://github.com/Becksteinlab/zarrtraj/blob/d4ab7710ec63813750d7224fe09bf5843e513570/joss_paper/figure_2.ipynb) for full benchmark codes. \label{fig:RMSD}](RMSD.png)
![RMSD benchmarks performed on the same machine as \autoref{fig:benchmark}. YiiP trajectory aligned to first frame as reference using `MDAnalysis.analysis.align.AlignTraj` and converted to compressed, quantized H5MD (7.8GB) and ZarrMD (4.9GB) trajectories. RMSD performed using development branch of MDAnalysis (2.8.0dev) with "serial" and "dask" backends. See [this notebook](https://github.com/Becksteinlab/zarrtraj/blob/883fcfa9337668dc4066de5548059d498560f647/joss_paper/figure_2.ipynb) for full benchmark codes. \label{fig:RMSD}](RMSD.png)

*Zarrtraj* is capable of making use of *Zarr*'s powerful compression and quantization when writing ZarrMD trajectories.
The uncompressed MDAnalysisData YiiP trajectory in ZarrMD format is reduced from 11.3GB uncompressed
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