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adding a notebook with first SPARQL queries
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NuriaQueralt committed Jun 6, 2024
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717 changes: 717 additions & 0 deletions .ipynb_checkpoints/metabolite_subsetting-checkpoint.ipynb

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122 changes: 122 additions & 0 deletions .ipynb_checkpoints/notebooks-checkpoint.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Content with notebooks\n",
"\n",
"You can also create content with Jupyter Notebooks. This means that you can include\n",
"code blocks and their outputs in your book.\n",
"\n",
"## Markdown + notebooks\n",
"\n",
"As it is markdown, you can embed images, HTML, etc into your posts!\n",
"\n",
"![](https://myst-parser.readthedocs.io/en/latest/_static/logo-wide.svg)\n",
"\n",
"You can also $add_{math}$ and\n",
"\n",
"$$\n",
"math^{blocks}\n",
"$$\n",
"\n",
"or\n",
"\n",
"$$\n",
"\\begin{aligned}\n",
"\\mbox{mean} la_{tex} \\\\ \\\\\n",
"math blocks\n",
"\\end{aligned}\n",
"$$\n",
"\n",
"But make sure you \\$Escape \\$your \\$dollar signs \\$you want to keep!\n",
"\n",
"## MyST markdown\n",
"\n",
"MyST markdown works in Jupyter Notebooks as well. For more information about MyST markdown, check\n",
"out [the MyST guide in Jupyter Book](https://jupyterbook.org/content/myst.html),\n",
"or see [the MyST markdown documentation](https://myst-parser.readthedocs.io/en/latest/).\n",
"\n",
"## Code blocks and outputs\n",
"\n",
"Jupyter Book will also embed your code blocks and output in your book.\n",
"For example, here's some sample Matplotlib code:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from matplotlib import rcParams, cycler\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"plt.ion()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Fixing random state for reproducibility\n",
"np.random.seed(19680801)\n",
"\n",
"N = 10\n",
"data = [np.logspace(0, 1, 100) + np.random.randn(100) + ii for ii in range(N)]\n",
"data = np.array(data).T\n",
"cmap = plt.cm.coolwarm\n",
"rcParams['axes.prop_cycle'] = cycler(color=cmap(np.linspace(0, 1, N)))\n",
"\n",
"\n",
"from matplotlib.lines import Line2D\n",
"custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),\n",
" Line2D([0], [0], color=cmap(.5), lw=4),\n",
" Line2D([0], [0], color=cmap(1.), lw=4)]\n",
"\n",
"fig, ax = plt.subplots(figsize=(10, 5))\n",
"lines = ax.plot(data)\n",
"ax.legend(custom_lines, ['Cold', 'Medium', 'Hot']);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"There is a lot more that you can do with outputs (such as including interactive outputs)\n",
"with your book. For more information about this, see [the Jupyter Book documentation](https://jupyterbook.org)"
]
}
],
"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": "3.10.9"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
"nbformat_minor": 4
}
122 changes: 122 additions & 0 deletions .ipynb_checkpoints/notebooks_original-checkpoint.ipynb
Original file line number Diff line number Diff line change
@@ -0,0 +1,122 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Content with notebooks\n",
"\n",
"You can also create content with Jupyter Notebooks. This means that you can include\n",
"code blocks and their outputs in your book.\n",
"\n",
"## Markdown + notebooks\n",
"\n",
"As it is markdown, you can embed images, HTML, etc into your posts!\n",
"\n",
"![](https://myst-parser.readthedocs.io/en/latest/_static/logo-wide.svg)\n",
"\n",
"You can also $add_{math}$ and\n",
"\n",
"$$\n",
"math^{blocks}\n",
"$$\n",
"\n",
"or\n",
"\n",
"$$\n",
"\\begin{aligned}\n",
"\\mbox{mean} la_{tex} \\\\ \\\\\n",
"math blocks\n",
"\\end{aligned}\n",
"$$\n",
"\n",
"But make sure you \\$Escape \\$your \\$dollar signs \\$you want to keep!\n",
"\n",
"## MyST markdown\n",
"\n",
"MyST markdown works in Jupyter Notebooks as well. For more information about MyST markdown, check\n",
"out [the MyST guide in Jupyter Book](https://jupyterbook.org/content/myst.html),\n",
"or see [the MyST markdown documentation](https://myst-parser.readthedocs.io/en/latest/).\n",
"\n",
"## Code blocks and outputs\n",
"\n",
"Jupyter Book will also embed your code blocks and output in your book.\n",
"For example, here's some sample Matplotlib code:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from matplotlib import rcParams, cycler\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"plt.ion()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Fixing random state for reproducibility\n",
"np.random.seed(19680801)\n",
"\n",
"N = 10\n",
"data = [np.logspace(0, 1, 100) + np.random.randn(100) + ii for ii in range(N)]\n",
"data = np.array(data).T\n",
"cmap = plt.cm.coolwarm\n",
"rcParams['axes.prop_cycle'] = cycler(color=cmap(np.linspace(0, 1, N)))\n",
"\n",
"\n",
"from matplotlib.lines import Line2D\n",
"custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),\n",
" Line2D([0], [0], color=cmap(.5), lw=4),\n",
" Line2D([0], [0], color=cmap(1.), lw=4)]\n",
"\n",
"fig, ax = plt.subplots(figsize=(10, 5))\n",
"lines = ax.plot(data)\n",
"ax.legend(custom_lines, ['Cold', 'Medium', 'Hot']);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"There is a lot more that you can do with outputs (such as including interactive outputs)\n",
"with your book. For more information about this, see [the Jupyter Book documentation](https://jupyterbook.org)"
]
}
],
"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": "3.10.14"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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2 changes: 1 addition & 1 deletion _build/html/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 5b9cfd08ffd10e13d688858e3c42551d
config: 8e2a1daa6ba7f8792b36e7fab37db85c
tags: 645f666f9bcd5a90fca523b33c5a78b7
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