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adding a notebook with first SPARQL queries
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.ipynb_checkpoints/metabolite_subsetting-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 | ||
} |
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Original file line number | Diff line number | Diff line change |
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@@ -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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# 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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