\n",
+ "
\n",
+ " \n",
+ "
\n",
+ "\n",
+ "\n",
+ "The *figure* and *image* directives work in the Jupyter Book but not locally (yet):\n",
"\n",
" \n",
"
\n",
@@ -30,18 +49,10 @@
"height: 300px\n",
"name: directive-fig\n",
"---\n",
- "Here is my figure caption!\n",
+ "Research Vessel Revelle (Scripps)\n",
"```\n",
" \n",
"
\n",
- " \n",
- "Markdown B: Use a more complicated back-tick construct to show the Revelle:\n",
- "\n",
- "\n",
- " \n",
- "image construct Try 1\n",
- " \n",
- "\n",
"
\n",
"\n",
"\n",
@@ -75,42 +86,58 @@
"```\n",
" \n",
"
\n",
+ "
\n",
+ "
\n",
"\n",
- " \n",
- "Bang Try 1\n",
"\n",
+ "Here is the `![alt](link)` construct which works locally and in the Book.\n",
+ "Down side: Renders are actual size.\n",
+ "\n",
+ "
\n",
+ "
\n",
" \n",
"![Revelle](../../img/revelle.jpg)\n",
"\n",
+ "
\n",
+ "
\n",
"\n",
"![Badge](../../img/use_case_badge.svg)\n",
"\n",
+ "
\n",
+ "
\n",
"\n",
"![Dubious](../../img/dubious.png)\n",
"\n",
+ "
\n",
+ "
\n",
+ "\n",
+ "\n",
+ "## Themes\n",
+ "\n",
+ "\n",
+ "Geo-SMART Jupyter Book theme placeholders:\n",
"\n",
- "### To Do\n",
- "\n",
- "- Cover the default chapter purposes here; and chart out the TOC properly, align the notebooks\n",
- " - These were deleted from the Jupyter Book 'chapters' folder `_toc.yml` file\n",
- " - file: chapters/motivation\n",
- " - file: chapters/methods\n",
- " - file: chapters/data\n",
- " - file: chapters/development\n",
- " - file: chapters/training\n",
- " - file: chapters/evaluation\n",
- " - file: chapters/workflow\n",
- " - file: chapters/reproducibility\n",
- " - file: chapters/conclusion\n",
- " - file: chapters/todo\n",
- " - file: chapters/questions\n",
- " - file: chapters/troubleshooting\n",
+ "\n",
+ "- Motivation: Create an access path to multiple views of ocean near-surface processes\n",
+ "- Method: Document the data acquisition and analysis process\n",
+ "- Development history: This project has been underway since 2016\n",
+ "- Training/Evaluation: Typically refers to ML; not present here yet\n",
+ "- Workflow\n",
+ "- Reproducibility\n",
+ "- Questions\n",
+ "- To Do\n",
+ "- Conclusion\n",
+ "- Troubleshooting\n",
" \n",
"\n",
- "### Introduction\n",
+ "## Introduction\n",
"\n",
"\n",
- "Let's begin with **Chlorophyll** as a convenient fluorescing marker in the larger context of **marine ecology**.\n",
+ "The ocean is water and salt; as well as being a reservoir of carbon compounds that\n",
+ "are the basis for and byproducts of ocean life. Our objective is to explore observational\n",
+ "data from the ocean with the idea of developing insights into the physical, chemical\n",
+ "and biological processes in the surface waters that are illuminated by sunlight. \n",
+ "Let's begin with a table of molecules; as a start on ocean chemistry.\n",
"\n",
" \n",
"| Mass (Daltons) | Substance\n",
@@ -120,167 +147,8 @@
"|62|carbonic acid H
2CO
3\n",
"|61|bicarbonate anion HCO
3-\n",
"|60|carbonate CO
32-\n",
- "|?|sugars here\n",
- "|894|chlorophyll C
55H
72MgN
4O
5\n",
- " \n",
- " \n",
- "The ocean is (of course) more than mere water and salt; it is a reservoir of carbon compounds that\n",
- "are the basis for and byproducts of ocean life."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 8,
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "
\n",
- "This Python cell uses %%html cell magic to support html. \n",
- "
\n",
- "The ocean is (of course) more than mere water and salt; it is a reservoir of carbon compounds that\n",
- "are the basis for and byproducts of ocean life.\n",
- "
\n",
- "
\n",
- "Through a molecular\n",
- "chemistry lens ocean carbon is both basis for and currency of life. The table below \n",
- "lists some important chemical constituents of the ocean sorted by mass. \n",
- "The heaviest of these, **chlorophyll**, is a convenient fluorescing marker in the \n",
- "context of **marine ecology**.\n",
- "
\n",
- "\n",
- "\n",
- "\n",
- "\n",
- "
\n",
- " \n",
- " Mass | \n",
- " Chemical | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " Hydrogen ion H+ | \n",
- "
\n",
- " \n",
- " 32 | \n",
- " dissolved oxygen O2 | \n",
- "
\n",
- " \n",
- " 46 | \n",
- " carbon dioxide CO2 | \n",
- "
\n",
- " \n",
- " 62 | \n",
- " carbonic acid H2CO3 | \n",
- "
\n",
- " \n",
- " 61 | \n",
- " bicarbonate anion HCO3- | \n",
- "
\n",
- " \n",
- " 60 | \n",
- " carbonate CO32- | \n",
- "
\n",
- " \n",
- " 180 | \n",
- " glucose C6H12O6 | \n",
- "
\n",
- " \n",
- " 892 | \n",
- " chlorophyll C55H72MgN4O5 | \n",
- "
\n",
- "
\n",
- "\n",
- "\n",
- "\n"
- ],
- "text/plain": [
- "
"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "%%html\n",
- "\n",
- "
\n",
- "This Python cell uses %%html cell magic to support html. \n",
- "
\n",
- "The ocean is (of course) more than mere water and salt; it is a reservoir of carbon compounds that\n",
- "are the basis for and byproducts of ocean life.\n",
- "
\n",
- "
\n",
- "Through a molecular\n",
- "chemistry lens ocean carbon is both basis for and currency of life. The table below \n",
- "lists some important chemical constituents of the ocean sorted by mass. \n",
- "The heaviest of these, **chlorophyll**, is a convenient fluorescing marker in the \n",
- "context of **marine ecology**.\n",
- "
\n",
- "\n",
- "\n",
- "\n",
- "\n",
- " \n",
- " \n",
- " Mass | \n",
- " Chemical | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " Hydrogen ion H+ | \n",
- "
\n",
- " \n",
- " 32 | \n",
- " dissolved oxygen O2 | \n",
- "
\n",
- " \n",
- " 46 | \n",
- " carbon dioxide CO2 | \n",
- "
\n",
- " \n",
- " 62 | \n",
- " carbonic acid H2CO3 | \n",
- "
\n",
- " \n",
- " 61 | \n",
- " bicarbonate anion HCO3- | \n",
- "
\n",
- " \n",
- " 60 | \n",
- " carbonate CO32- | \n",
- "
\n",
- " \n",
- " 180 | \n",
- " glucose C6H12O6 | \n",
- "
\n",
- " \n",
- " 892 | \n",
- " chlorophyll C55H72MgN4O5 | \n",
- "
\n",
- "
\n",
- "\n",
- "\n",
- "\n"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* FASTQ sequence file format\n",
- "* Do prisoners hats: Were you paying attention?\n",
- "* Magda still interested?\n",
- "* CRC and Hamming\n",
- "* S3 non-object access\n",
- "* What about a question for which there is no computer code... but then that code gets written\n",
- "* Hofstadter self-destroying turntable (Luddites using wrenches from loom builders)\n",
- "* Talk to Wendi about using a zar API"
+ "|180|glucose C6H12O6\n",
+ "|894|chlorophyll C55H72MgN4O5"
]
},
{
@@ -449,11 +317,13 @@
"### Metabolic energy for an apex predator\n",
"\n",
"\n",
- "
\n",
- "\n",
- "\n",
- "
\n",
- "\n",
+ "```{figure} ../../img/Sphyrna_mokarran.png.jpg\n",
+ "---\n",
+ "height: 500px\n",
+ "name: directive-fig\n",
+ "---\n",
+ "Apex predator: Great hammerhead shark (Sphyrna mokarran)\n",
+ "```\n",
" \n",
"Sunlight is not a direct energy source for \n",
"[Sphyrna mokarran](https://en.wikipedia.org/wiki/Great_hammerhead))\n",