post review edits/enhancements

Author: j-atkins

docs/user-guide/assignments/Sail_the_ship.ipynb

@@ -59,7 +59,7 @@
    "source": [
     "## Your virtual expedition...\n",
     "\n",
-    "This guide will help you get started with running your VirtualShip expedition. Follow the steps below to set up your programming environment, configure your expedition, and launch your simulation. \n",
+    "Now let's get started on running your VirtualShip expedition. Follow the steps below to set up your coding environment, plan your expedition, and launch your simulation. \n",
     "\n",
     "<div class=\"alert alert-block alert-warning\"> \n",
     "Before that though, make sure you have had your research question approved by your instructor!\n",
@@ -101,7 +101,7 @@
     "\n",
     "### NIOZ MFP tool\n",
     "\n",
-    "The first step is to plan the expedition route for your chosen research question, bearing in mind where you will need to go to collect data for your research, what kind of sampling strategy you will use, and how long you want your expedition to last (remember, though, you have a three week ship time limit).\n",
+    "The first step is to plan the expedition route for your chosen research question, bearing in mind the time needed for your sampling strategy, and traveling to and from a port suitable for research vessels (remember though, you have a three week ship time limit).\n",
     "\n",
     "Your route can be created with the online [NIOZ MFP tool](https://nioz.marinefacilitiesplanning.com/cruiselocationplanning#). Documentation on how to use the website can be found [here](https://surfdrive.surf.nl/files/index.php/s/84TFmsAAzcSD56F). Alternatively, you can watch this [video](https://www.youtube.com/watch?v=yIpYX2xCvsM&list=PLE-LzO7kk1gLM74U4PLDh8RywYXmZcloz&ab_channel=VirtualShipClassroom), which runs through how to use the MFP tool.\n",
     "\n",
@@ -112,11 +112,11 @@
     "\n",
     "### Upload the coordinates to your virtual machine\n",
     "\n",
-    "<div class=\"alert alert-block alert-success\"> \n",
-    "**TIP**: If you have not done so already, make sure you create a folder for your group's expedition data in your persistent storage on SURF RC (i.e. `mkdir data/storage-osl/{your-group-name}`).\n",
+    "<div class=\"alert alert-block alert-warning\"> \n",
+    "**IMPORTANT**: _If you have not done so already_, make sure you create a folder for your group's expedition data in the persistent storage on SURF RC (i.e. the `data/storage-osl/` folder). You can do so by running `mkdir /data/storage-osl/{your-group-name}` in Terminal, replacing `{your-group-name}` with your actual group name, or by using the \"New Folder\" button in the JupyterLab file explorer panel.\n",
     "</div>\n",
     "\n",
-    "Back in the SURF RC JupyterLab interface, use the file explorer on the left hand side to navigate to the directory where your group will be running your expedition (i.e. `data/storage-osl/{your-group-name}`). \n",
+    "Back in the SURF RC JupyterLab interface, use the **file explorer** on the left hand side to navigate to the directory where your group will be running your expedition (i.e. `data/storage-osl/{your-group-name}`). \n",
     "\n",
     "Then upload the exported .xlsx file (it will be called something like \"Coordinates-20251125T1403.xlsx\") by either dragging and dropping it from your laptop's Downloads into the file explorer, or by using the \"Upload Files\" button (the icon with an upward arrow) at the top of the file explorer panel."
    ]
@@ -129,11 +129,13 @@
     "\n",
     "Open a Terminal window if you do not already have one open. Remember, this can be done from the Launcher tab by clicking on \"Terminal\" button under the \"Other\" section, or by going to the \"File\" menu --> \"New\" --> \"Terminal\".\n",
     "\n",
-    "Once in Terminal, navigate to where you would like your expedition to be run on your (virtual) machine (i.e. `cd data/storage-osl/{your-group-name}`). Then enter the following command in the Terminal (changing `EXPEDITION_NAME` to something more meaningful for your group's expedition):\n",
+    "<div class=\"alert alert-block alert-warning\"> \n",
+    "**IMPORTANT**: Once in Terminal, navigate to where you would like your expedition to be run on your (virtual) machine. You can do so by `cd /data/storage-osl/{your-group-name}`, replacing `{your-group-name}` with your actual group name. This is where you will be working from for the rest of the session.\n",
+    "</div>\n",
+    "\n",
+    "Now enter the following command in the Terminal (changing `EXPEDITION_NAME` to something more meaningful for your group's expedition):\n",
     "\n",
-    "```\n",
-    "virtualship init EXPEDITION_NAME --from-mfp {CoordinatesExport}.xlsx\n",
-    "```\n",
+    "`virtualship init EXPEDITION_NAME --from-mfp {CoordinatesExport}.xlsx`\n",
     "\n",
     "<div class=\"alert alert-block alert-success\"> \n",
     "**TIP**: The `{CoordinatesExport}.xlsx` in the command above refers to the .xlsx file exported from MFP and uploaded to your virtual machine earlier. Replace the filename with the name of your .xlsx file.\n",
@@ -149,7 +151,7 @@
     "## 5) Expedition scheduling & ship configuration\n",
     "\n",
     "<div class=\"alert alert-block alert-success\"> \n",
-    "**TIP**: From here, you should replace any references to `EXPEDITION_NAME` with the actual name you used for your expedition when running the `virtualship init` command.\n",
+    "**TIP**: From here, you should replace any references to `EXPEDITION_NAME` with the actual name you used for your expedition when running any `virtualship` commands.\n",
     "</div>\n",
     "\n",
     "The next step is to finalise the expedition schedule plan, including setting times and instrument selection choices for each waypoint, as well as configuring the ship (including any underway measurement instruments). \n",
@@ -205,7 +207,7 @@
     "</div>\n",
     "\n",
     "<div class=\"alert alert-block alert-warning\"> \n",
-    "**CAUTION**: The `virtualship plan` tool will check that the ship can reach each waypoint according to the prescribed ship speed (10 knots). However, before the ultimate [simulation step](#run-the-expedition) there will be a final, automated check that the schedule also accounts for the time taken to conduct the measurements at each site (e.g. a CTD cast in deeper waters will take longer). Therefore, we recommend to take this extra time into account at this stage of the planning by estimating how long each measurement will take and adding this time on.\n",
+    "**CAUTION**: The `virtualship plan` tool will check that the ship can reach each waypoint according to the prescribed ship speed (10 knots). However, before the ultimate simulation step (i.e. step 6 below) there will be a final, automated check that the schedule also accounts for the time taken to conduct the measurements at each site (e.g. a CTD cast in deeper waters will take longer). Therefore, we recommend to take this extra time into account at this stage of the planning by estimating how long each measurement will take and adding this time on.\n",
     "</div>"
    ]
   },
@@ -218,10 +220,12 @@
     "You are now ready to run your virtual expedition! This stage will take all the measurements for each of instruments you selected at each waypoint in your expedition schedule, using input data sourced from the [Copernicus Marine Data Store](https://data.marine.copernicus.eu/products).\n",
     "\n",
     "<div class=\"alert alert-block alert-info\"> \n",
-    "**NOTE**: You will need to register for Copernicus Marine Service account (see [here](https://data.marine.copernicus.eu/register)), if you have not done so already.\n",
+    "**NOTE**: You will need to register for a Copernicus Marine Service account (you can do so [here](https://data.marine.copernicus.eu/register)), if you have not done so already.\n",
     "</div>\n",
     "\n",
-    "You can run your expedition simulation using the command: `virtualship run EXPEDITION_NAME`\n",
+    "You can run your expedition simulation using the command: \n",
+    "\n",
+    "`virtualship run EXPEDITION_NAME`\n",
     "\n",
     "If this is your first time running VirtualShip, you will be prompted to enter your own Copernicus Marine Data Store credentials (these will be saved automatically for future use).\n",
     "\n",