SURF instructions documentation updates

docs/user-guide/tutorials/surf_research_cloud_setup.ipynb

@@ -31,7 +31,7 @@
     "Note: This only needs to be done once during setup.\n",
     "```\n",
     "\n",
-    "In the Jupyter workspace, you'll see the following in your file explorer:\n",
+    "In the Jupyter workspace, you'll see the following (or similar) in your file explorer:\n",
     "\n",
     "```\n",
     ".\n",
@@ -42,17 +42,21 @@
     "└── scratch\n",
     "```\n",
     "\n",
-    "The `data/shared-storage` folder is your persistent storage. Here you can make a folder (e.g., `mkdir data/shared-storage/{your-group-name}` replacing `{your-group-name}` with your group name) to house your work for the unit. This folder will be visible to anyone using the workspace, but only you will be able to make edits to it. This is the primary place you should store your `virtualship` configs and content relevant to this unit.\n",
+    "__Note__: the persistent storage folder may be called something slightly different in your instance, for example it may have a name specific to the course you are enrolled on, such as `data/storage-1-sept`.\n",
+    "\n",
+    "In the Jupyter launcher, you can open a Terminal session by clicking on the \"Terminal\" box. From here you can navigate the workspace directory structure and run commands.\n",
+    "\n",
+    "The `data/shared-storage` folder is your persistent storage. Here you can make a folder (e.g., by running `mkdir data/shared-storage/{your-group-name}` as a command in the Terminal, replacing `{your-group-name}` with your group name) to house your work for the unit. This folder will be visible to anyone using the workspace, but only you will be able to make edits to it. This is the primary place you should store your `virtualship` configs and content relevant to this unit.\n",
     "\n",
     "---\n",
     "\n",
-    "To be able to run VirtualShip from the Terminal, we need to take some additional steps which are detailed in the `KERNEL-README.ipynb`. This contains important information for configuring your environment. Namely, for our uses, the \"Initialize conda\" section. Do the following:\n",
+    "To be able to run VirtualShip from the Terminal, we need to take some additional steps which are detailed in the `KERNEL-README.ipynb`. This contains important information for configuring your environment. Specifically, for our uses, the \"Initialize conda\" section (also copied below). Do the following:\n",
     "\n",
     "#### Initialize conda\n",
     "\n",
     "To make the already installed conda-tool available for yourself, you have to initialize your Terminal shell.\n",
     "\n",
-    "Start a \"Terminal\" tab in the Jupyter Lab launcher and type: `/etc/miniconda/bin/conda init`\n",
+    "Back in the \"Terminal\" tab, type: `/etc/miniconda/bin/conda init`\n",
     "\n",
     "Close the Terminal tab and start a new one.\n",
     "You will see that the Terminal prompt has changed to something like\n",
@@ -76,10 +80,12 @@
     "\n",
     "Here you can do `conda activate virtualship` to activate the environment called \"virtualship\". This environment is a shared environment among all workspace users that can be centrally updated. If you want, you can create and manage your own environments by running the relevant conda commands.\n",
     "\n",
-    "With the `virtualship` environment, you now have access to the `virtualship` command in your Terminal, which can be confirmed by running `virtualship --help`. From here you can `cd` into `data/shared-storage/{your-name}` and run `virtualship` commands as you would on your local machine.\n",
+    "With the `virtualship` environment, you now have access to the `virtualship` command in your Terminal, which can be confirmed by running `virtualship --help`. From here you can `cd` into `data/shared-storage/{your-name}` and run `virtualship` commands as you would on your local machine (see the VirtualShip [quickstart guide](https://virtualship.readthedocs.io/en/latest/user-guide/quickstart.html)). \n",
     "\n",
     "---\n",
     "\n",
+    "## Working in Jupyter Notebooks\n",
+    "\n",
     "Finally, when you're working in Jupyter Notebooks, you are able to access the Conda environment with `virtualship` and related dependencies by switching the Kernel in the top right of the UI.\n",
     "\n",
     "\n",