semantics

Becksteinlab · Oct 3, 2024 · 9e00912 · 9e00912
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commit 9e00912
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/joss_paper/paper.md b/joss_paper/paper.md
@@ -130,9 +130,9 @@ at roughly 1/2 or 1/3 the speed it can iterate through the same trajectory from
 However, it should be noted that this speed is influenced by network latency and that
 writing parallelized algorithms can offset this loss of speed as in \autoref{fig:RMSD}. 
 
-![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. \label{fig:benchmark}](benchmark.png)
+![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]() 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/d4ab7710ec63813750d7224fe09bf5843e513570/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