added example

docs/source/index.rst

@@ -16,9 +16,9 @@ This means users can interact with massive trajectory files without ever storing
    :caption: Contents:
 
    installation
+   yiip_example
    walkthrough
    api
    performance_considerations
-   zarrmd-file-spec/v0.2.0
    benchmarks
 

docs/source/yiip_example.rst

@@ -0,0 +1,29 @@
+YiiP Protein Example
+====================
+
+To get started immediately with *Zarrtraj*, we have made the topology and trajectory of the 
+[YiiP protein in a POPC membrane](https://www.mdanalysis.org/MDAnalysisData/yiip_equilibrium.html)
+publicly available for streaming. The trajectory is stored in in the `zarrmd` format 
+for optimal streaming performance. 
+
+To access the trajectory, follow this example:
+
+```python
+import zarrtraj
+import MDAnalysis as mda
+import fsspec
+
+
+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:
+        # Do something
+```
+
+While there is not yet an officially recommended way to access cloud-stored topologies, this
+method of opening a Python `File`-like object from the topology URL in PDB format using *FSSpec*
+works with MDAnalysis 2.7.0. Check back later for further development!

joss_paper/paper.md

@@ -9,32 +9,35 @@ tags:
 authors:
   - name: Lawson Woods
     orcid: 0009-0003-0713-4167
-    affiliation: [3, 4]
-  - name: Hugo Macdermott-Opeskin
+    affiliation: [1, 2]
+  - name: Hugo MacDermott-Opeskin
     orcid: 0000-0002-7393-7457
+    affiliation: [3]
   - name: Edis Jakupovic 
-    affiliation: [1, 2]
+    affiliation: [4, 5]
   - name: Yuxuan Zhuang
     orcid: 0000-0003-4390-8556
-    affiliation: [5, 6]
+    affiliation: [6, 7]
   - name: Richard J Gowers
     orcid: 0000-0002-3241-1846
   - name: Oliver Beckstein
     orcid: 000-0003-1340-0831
-    affiliation: [1, 2]
+    affiliation: [4, 5]
 affiliations:
- - name: Department of Physics, Arizona State University, Tempe, Arizona, United States of America
+ - name: School of Computing and Augmented Intelligence, Arizona State University, Tempe, Arizona, United States of America
    index: 1
- - name: Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America
+ - name: School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
    index: 2
- - name: School of Computing and Augmented Intelligence, Arizona State University, Tempe, Arizona, United States of America
+ - name: Open Molecular Software Foundation, Davis, CA, United States of America
    index: 3
- - name: School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
+ - name: Center for Biological Physics, Arizona State University, Tempe, AZ, United States of America
    index: 4
- - name: Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
+ - name: Department of Physics, Arizona State University, Tempe, Arizona, United States of America
    index: 5
- - name: Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
+ - name: Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
    index: 6
+ - name: Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
+   index: 7
 date: 22 September 2024
 bibliography: paper.bib
 ---
@@ -140,6 +143,10 @@ to just 4.9GB after compression with the Zstandard algorithm [@Zstandard:2021]
 and quantization to 3 digits of precision. See [performance considerations](https://zarrtraj.readthedocs.io/en/latest/performance_considerations.html)
 for more.
 
+# Example
+
+The YiiP membrane protein trajectory [@YiiP:2019] used for benchmarking in this paper is publicly available for streaming from the Google Cloud Bucket *"gcs://zarrtraj-test-data"*. To access it, 
+follow the up-to-date instructions [here](https://zarrtraj.readthedocs.io/en/latest/yiip_example.html).
 
 # Acknowledgements