Add assignment for an ECR expedition proposal (#113)

* Add assignment for an ECR expedition proposal * fix link and add scicom to index * create shared intro * thumbnails * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * changes titles * trying from _images folder * with links * spelling * assignments folder * assignment folder --------- Co-authored-by: Emma Daniels <[email protected]> Co-authored-by: Emma Daniels <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
OceanParcels · Feb 6, 2025 · edccedb · edccedb
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diff --git a/docs/conf.py b/docs/conf.py
@@ -70,3 +70,10 @@
 ]
 
 always_document_param_types = True
+
+nbsphinx_thumbnails = {
+    "user-guide/assignments/Research_proposal_intro": "user-guide/_images/MFPtimeline.jpg",
+    "user-guide/assignments/Research_Proposal_only": "user-guide/_images/MFP.jpg",
+    "user-guide/assignments/Virtualship_research_proposal": "user-guide/_images/AnnaWeber.jpeg",
+    "user-guide/assignments/sciencecommunication_assignment": "user-guide/_images/marine_ss.jpg",
+}
diff --git a/docs/user-guide/_images/AnnaWeber.jpeg b/docs/user-guide/_images/AnnaWeber.jpeg
diff --git a/docs/user-guide/_images/MFP.jpg b/docs/user-guide/_images/MFP.jpg
diff --git a/docs/user-guide/_images/MFPtimeline.jpg b/docs/user-guide/_images/MFPtimeline.jpg
diff --git a/docs/user-guide/_images/links.ipynb b/docs/user-guide/_images/links.ipynb
@@ -0,0 +1,24 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[AnnaWeber](AnnaWeber.jpeg)\n",
+    "\n",
+    "[MFP_planning](MFP.jpg)\n",
+    "\n",
+    "[MFP_timeline](MFPtimeline.jpg)\n",
+    "\n",
+    "[Marine_soft_skills](marine_ss.jpg)"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/docs/user-guide/_images/marine_ss.jpg b/docs/user-guide/_images/marine_ss.jpg
diff --git a/docs/user-guide/assignments/Research_Proposal_only.ipynb b/docs/user-guide/assignments/Research_Proposal_only.ipynb
@@ -0,0 +1,276 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Research Proposal for student grant"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "***"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Please read the [Introduction](./Research_proposal_intro.ipynb) and fill out the Proposal below."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Proposal "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Project Data\n",
+    "1. **Title of the proposal**\n",
+    "\n",
+    "Please choose an appropriate and concise title for the expedition that refers to the work area. \n",
+    "\n",
+    "2. **Cruise participants**\n",
+    "\n",
+    "Please provide a list of anticipated cruise participants. Include at least your own names. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Methodology"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "3. **Research question**\n",
+    "\n",
+    "Please provide a clear and measurable research question. \n",
+    "\n",
+    "Here are some examples of research you can use as inspiration: \n",
+    "\n",
+    "[The Irminger Gyre: Circulation, convection, and interannual variability](https://doi.org/10.1016/j.dsr.2011.03.001)\n",
+    "\n",
+    "[Argo float observations of basin-scale deep convection in the Irminger sea during winter 2011–2012](https://doi.org/10.1016/j.dsr.2015.12.012)\n",
+    "\n",
+    "\n",
+    "<i>Note that your question does not have to be novel. The most important is that it is researchable with the expedition planned here.  <i>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "4. **Study area**\n",
+    "\n",
+    "Please explain why you chose this research topic and how the anticipated outcomes of your research contribute to our understanding. Word limit: 300.   "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "5. **Choice of vessel**\n",
+    "\n",
+    "Please state the preferred research vessel for this cruise. \n",
+    "Choose from https://www.nioz.nl/national-marine-facilities/research-vessels \n",
+    "\n",
+    "If the NIOZ vessels don’t suffice, pick any of the ships available through MFP and explain why you need this ship. https://nioz.marinefacilitiesplanning.com/programme \n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "6. **Scientific equipment required**\n",
+    "   \n",
+    "Please tick both on-board and external equipment needed during the cruise. Note that you can only use one of the ADCPs at any time.   \n",
+    "<small><i>To check a box, replace [  ] with [x].</i></small>\n",
+    "\n",
+    "- [ ] Underway Data\n",
+    "      \n",
+    "- [ ] ADCP (OceanObserver max depth 1000m with data every 24 meters) \n",
+    "\n",
+    "- [ ] ADCP (SeaSeven max depth 150m with data every 4 meters) \n",
+    "\n",
+    "- [ ] XBTs\n",
+    "\n",
+    "- [ ] CTD \n",
+    "\n",
+    "- [ ] Argo floats \n",
+    "\n",
+    "- [ ] Drifters \n",
+    "\n",
+    "Please explain why you use the instruments checked above. Word limit: 300."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Cruise Data\n",
+    "\n",
+    "A map and cruise plan can be created through [the NIOZ MFP website](https://nioz.marinefacilitiesplanning.com/cruiselocationplanning#)\n",
+    "\n",
+    "Documentation on how to use the website can be found [here](https://surfdrive.surf.nl/files/index.php/s/84TFmsAAzcSD56F) and you can watch the video below.\n",
+    "<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/yIpYX2xCvsM?si=sEXq0Zn5z94JJ3yE\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen></iframe>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "7. **Cruise period**\n",
+    "\n",
+    "Please state the preferred year, season, and/or month(s) for the cruise, and provide reasons for restrictions to limited periods. \n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "8. **Map of working area**\n",
+    "\n",
+    "Please upload a high-resolution map of the oceans areas you'll research and inlcude all stations and transects.  "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "9. **Cruise departure and arrival port; and transit days**\n",
+    "\n",
+    "Please name your preferred port of departure and preferred port of arrival. \n",
+    "\n",
+    "Please enter the number of days required for transit from the preferred port of departure to the working area and the number of days required for transit from the working area to the preferred port of arrival, each rounded to the nearest whole number. Please note that transit times from the port of departure to the first station and from the last station in the working area to the port of arrival are regarded as work days at sea, so they are deducted from your three-week availability. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "10. **Working areas / EEZs**\n",
+    "\n",
+    "Please indicate all nations from which research permits would need to be obtained on the basis of planned work in the respective Exclusive Economic Zones (EEZs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "11. **Scientific work program**\n",
+    "\n",
+    "Please provide a scheme with number of necessary work and in-transit days within the working areas and station times. This can be downloaded from [the NIOZ MFP website](https://nioz.marinefacilitiesplanning.com/cruiselocationplanning#) using the Export button on the right.\n",
+    "\n",
+    "Please indicate at each station what instruments you want to deploy (CTD, Argo float, drifter, XBT) and take the deployment time into account. If you plan to use Argo floats, please give the required depth and cycle duration. In case of the CTD the deployment time depends on the depth of the ocean. \n",
+    "\n",
+    "Here is some sample code to sample the depth using the bathymetry data that the Virtual Ship will also use. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# example for plotting and querying bathymetry data\n",
+    "# Download data\n",
+    "import requests\n",
+    "\n",
+    "files = {\n",
+    "    \"GLO-MFC_001_024_mask_bathy.nc\": \"https://surfdrive.surf.nl/files/index.php/s/AdbtlgP3LJv6tOn/download\",\n",
+    "}\n",
+    "\n",
+    "for filename, url in files.items():\n",
+    "    response = requests.get(url, allow_redirects=True)\n",
+    "\n",
+    "if response.status_code == 200:\n",
+    "    with open(filename, \"wb\") as f:\n",
+    "        f.write(response.content)\n",
+    "\n",
+    "else:\n",
+    "    print(\"Failed to download\", url)\n",
+    "print(\"Download ready\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import cartopy.crs as ccrs\n",
+    "import xarray as xr\n",
+    "\n",
+    "# Load the bathymetry data using xarray\n",
+    "data = xr.open_dataset(\"GLO-MFC_001_024_mask_bathy.nc\")\n",
+    "\n",
+    "# Create a bathymetry figure and axis with Cartopy projection\n",
+    "fig, ax = plt.subplots(figsize=(15, 5), subplot_kw={\"projection\": ccrs.PlateCarree()})\n",
+    "data.deptho.plot(ax=ax, cmap=\"viridis\")\n",
+    "\n",
+    "# Specify extent, add gridlines and coastlines, show plot\n",
+    "ax.set_extent(\n",
+    "    (130, 160, -70, -40), crs=ccrs.PlateCarree()\n",
+    ")  # set extent as (x0, x1, y0, y1)\n",
+    "ax.gridlines(draw_labels=True)\n",
+    "ax.coastlines()\n",
+    "plt.show()\n",
+    "\n",
+    "# Query and print the bathymetry data at the specified location\n",
+    "station_depth = data.deptho.sel(latitude=-50, longitude=150, method=\"nearest\")\n",
+    "print(f\"The depth at this station is: {station_depth.values} meters\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "12. **Feasibility**\n",
+    "\n",
+    "Please explain how the methodology detailed in this proposal aims to answer your research question. Word limit: 500."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "13. **Contingency**\n",
+    "\n",
+    "Please explain which stations/measurements you will skip in case of unforseen circumstances that delay your planning. Word limit: 300."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.15"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}