Update docs

docs/user-guide/assignments/Sail_the_ship.ipynb

@@ -251,10 +251,6 @@
     "\n",
     "Small simulations (e.g. small space-time domains and fewer instrument deployments) will be relatively fast. For large, complex expeditions, it _could_ take up to an hour to simulate the measurements depending on your choices. Waiting for simulation is a great time to practice your level of patience. A skill much needed in oceanographic fieldwork ;-)\n",
     "\n",
-    "<div class=\"alert alert-block alert-success\"> \n",
-    "**Tip**: Not using underway instruments will speed up the simulation time considerably. So, if you do not plan to use underway temperature/salinity or ADCP measurements, make sure to switch these off in the planning tool before running the expedition.\n",
-    "</div>\n",
-    "\n",
     "<div class=\"alert alert-block alert-warning\"> \n",
     "**Important**: VirtualShip may encounter 'real-life challenges' during the expedition, which simulate the various problems and unexpected events that can occur during real-life oceanographic expeditions (e.g. instrument and/or equipment failure, logistical challenges etc.). These may require your intervention to ensure your expedition schedule can continue!\n",
     "</div>"
@@ -266,11 +262,11 @@
    "source": [
     "## 7) Results\n",
     "\n",
-    "Upon successfully completing the simulation, results from the expedition will be stored in the `EXPEDITION_NAME/results` directory, written as [Zarr](https://zarr.dev/) files.\n",
+    "Upon successfully completing the simulation, results from the expedition will be stored in the `EXPEDITION_NAME/results` directory, written in `.parquet` [format](https://parquet.apache.org/).\n",
     "\n",
-    "From here you can carry on your analysis. In general, we encourage you to explore and analyse these data using [Xarray](https://docs.xarray.dev/en/stable/). We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments. Use these to help you get started!\n",
+    "From here you can carry on your analysis. In general, we encourage you to use [Parcels](https://Parcels-code.org/) (i.e. `parcels.read_particlefile()`) to read in VirtualShip output files, and tools such as [Polars](https://www.pola.rs/) and/or [Pandas](https://pandas.pydata.org/) for further data analysis. We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments. Use these to help you get started!\n",
     "\n",
-    "If you are using VirtualShip in class, the same tutorial notebooks will be uploaded in your SURF RC environment for you to use and interact directly with the code. These should be available in e.g. the `data/storage/tutorials/` directory. You will notice that there is a notebook file dedicated to visualising each of the different instruments available in VirtualShip. \n",
+    "If you are using VirtualShip in class, the same tutorial notebooks may be uploaded in your SURF RC environment for you to use and interact directly with the code. These should be available in e.g. the `data/storage/tutorials/` directory. You will notice that there is a notebook file dedicated to visualising each of the different instruments available in VirtualShip. \n",
     "\n",
     "To run these notebooks with your own data, you will need to copy the them over to your expedition working directory (i.e. `data/storage/{your-group-name}`). This can be done by either 1) using the file explorer panel in JupyterLab to copy the relevant files or the via the command line in Terminal. In the terminal, running `cp -r /data/storage/tutorials/* /data/storage/{your-group-name}/` would copy __all__ the tutorial notebooks to your group's directory, so if you only want to copy specific ones, make sure to adjust the command accordingly."
    ]

docs/user-guide/documentation/pre_download_data.md

@@ -77,6 +77,7 @@ The following assumptions are also made about the data:
 3. If using BGC-enabled instruments (e.g. BGC variables on the `CTD`), the relevant biogeochemical data files must contain the following variables: `o2`, `chl`, `no3`, `po4`, `nppv`, `ph`, `phyc`.
    - Or these strings must appear as substrings within the variable names (e.g. `o2_glor` is acceptable for `o2`).
 4. Bathymetry data files must contain a variable named `deptho`.
+5. Pre-downloaded data files must have a `"positive"` attribute for the depth dimension (e.g. `"positive": "down"` or `"positive": "up"`) in order to ensure that the depth dimension is correctly interpreted by Parcels under-the-hood.
 
 #### Also of note
 

docs/user-guide/index.md

@@ -18,5 +18,4 @@ documentation/full_sensor_list.md
 documentation/copernicus_products.md
 documentation/pre_download_data.md
 documentation/example_copernicus_download.ipynb
-documentation/full_sensor_list.md
 ```

docs/user-guide/quickstart.md

@@ -178,6 +178,8 @@ See the relevant [documentation](https://virtualship.readthedocs.io/en/latest/us
 
 ## 5) Results
 
-Upon successfully completing the simulation, results from the expedition will be stored in the `EXPEDITION_NAME/results` directory, written as [Zarr](https://zarr.dev/) files.
+Upon successfully completing the simulation, results from the expedition will be stored in the `EXPEDITION_NAME/results` directory, written in `.parquet` [format](https://parquet.apache.org/).
 
-From here you can carry on your analysis (offline). We encourage you to explore and analyse these data using [Xarray](https://docs.xarray.dev/en/stable/). We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments.
+From here you can carry on your analysis (offline). We encourage you to use [Parcels](https://Parcels-code.org/) (i.e. `parcels.read_particlefile()`) to read in VirtualShip output files, and tools such as [Polars](https://www.pola.rs/) and/or [Pandas](https://pandas.pydata.org/) for further data analysis.
+
+We also provide various [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) with further examples of how to visualise data recorded by the VirtualShip instruments.

docs/user-guide/teacher-content/index.md

@@ -1,5 +1,7 @@
 # Teacher content
 
+### Overview
+
 VirtualShip is used as part of the VirtualShip Classroom, that combines authentic tools with VR to create a virtual fieldwork experience and allows you to teach about sea-based research from your regular classroom.
 
 All VirtualShip Classroom (VSC) material is open under an MIT licence and freely available! You can use the VSC to teach anything from a 4 hour masterclass up to an open assignment of more than 40 hours. Example assignments are available below and please feel free to customize anything offline or [contribute](../../contributing/index.md) to the assignments provided here.
@@ -16,17 +18,26 @@ The VSC design focuses on creating didactically sound, authentic learning experi
 
 We evaluated in several (under)graduate courses and find that the VirtualShip Classroom is highly engaging, and students report on enhanced confidence and knowledge [(Daniels et al. 2025)](https://current-journal.com/articles/10.5334/cjme.121).
 
+### Teaching materials
+
 ```{toctree}
 :maxdepth: 1
-:caption: Teaching materials
 
 ILOs.ipynb
 letter.md
 ```
 
+### Previous implementations
+
+```{warning}
+The following implementations are examples of how the VSC has been used in the past. They are provided here for reference only and may not be up to date with the latest version of the VSC and/or VirtualShip software.
+```
+
+#### Utrecht University
+
 ```{nbgallery}
 ---
-caption: UU Ocean of the Future
+caption: Ocean of the Future (BSc), 2025-26
 ---
 UU-ocean-of-future/Tutorial1.ipynb
 UU-ocean-of-future/CoordinatesExport-Transect.xlsx
@@ -37,7 +48,7 @@ UU-ocean-of-future/plot_slider.py
 
 ```{nbgallery}
 ---
-caption: UU Dynamical Oceanography
+caption: Dynamical Oceanography (MSc), 2025-26
 ---
 UU-dyoc/example_expedition.md
 UU-dyoc/file_permissions.md