intro-to-jupyter-bme4550.ipynb

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    "# <center> An introduction to Jupyter notebooks </center>\n",
    "## <center> UVA BME4550 <br> September 14th 2020 </center>\n",
    "#### <center> Modified from [ECS Data Science Hack Week 2018](https://ecshackweek.github.io/tutorial/getting-started-with-jupyter/)</center>"
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   "source": [
    "## What is Jupyter?\n",
    "\n",
    "### It's a browser based application allowing you to run \"notebooks\" in your browser.\n",
    "### These notebooks can contain code"
   ]
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    "a = 42\n",
    "\n",
    "print(a)"
   ]
  },
  {
   "cell_type": "code",
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   "source": [
    "import datetime\n",
    "\n",
    "michiganStrikeStart = datetime.date(2020, 9, 8)\n",
    "now = datetime.datetime.now().date()\n",
    "\n",
    "print('University of Michigan Graduate Students have been striking for {} days!'.format((now-michiganStrikeStart).days))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## You can run bash commands (Must use `!`)"
   ]
  },
  {
   "cell_type": "code",
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   "outputs": [],
   "source": [
    "!echo \"This is a notebook\""
   ]
  },
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   "metadata": {},
   "source": [
    "## You can add images:"
   ]
  },
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   "source": [
    "<img src=\"https://pbs.twimg.com/profile_images/1299120224751562752/nGHJbhC8_400x400.jpg\" width=200 />\n",
    "<img src=\"https://pbs.twimg.com/media/Eg_Zqh7XcAAaEiq?format=jpg&name=large\" width=300 />"
   ]
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   "metadata": {},
   "source": [
    "## You can add Markdown Syntax:"
   ]
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   "source": [
    "### Lists\n",
    "- a\n",
    "- b \n",
    "\n",
    "### Equations\n",
    "$$\n",
    "\\frac{\\partial (\\epsilon c)}{\\partial t} = \\frac{\\partial}{\\partial x}\\left( \\epsilon D_{eff}\\frac{\\partial c}{\\partial x} \\right) + a (1-t_+^0) j_n\n",
    "$$\n",
    "\n",
    "### Tables\n",
    "\n",
    "| Name | | Column |\n",
    "|:---:|:---:|:---:|\n",
    "||This is a fun table||\n",
    "|To Do| Fill in the rest| |"
   ]
  },
  {
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   "source": [
    "# Easy development of code in bite size chunks"
   ]
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   "source": [
    "### Data intensive step"
   ]
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   "source": [
    "# import the pandas package\n",
    "import pandas as pd\n",
    "\n",
    "# read in the data from our file\n",
    "file_location = 'https://raw.githubusercontent.com/mdmurbach/ECS-Hack-Day-2017/master/time-data(833).txt?raw=true'\n",
    "data = pd.read_csv(file_location)\n",
    "\n",
    "# assign names to each of the columns for easy reference\n",
    "data.columns = ['time(s)', 'current(A)', 'potential(V)', 'frequency(Hz)', 'amplitude(A)']\n",
    "\n",
    "# print out the first 5 rows of our data\n",
    "data.head()"
   ]
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   "source": [
    "### Followed by a visualization or exploratory data analysis"
   ]
  },
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   "source": [
    "#Make sure matplotlib plots in the borwser\n",
    "%matplotlib inline \n",
    "\n",
    "# import the matplotlib package\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "# plot the current and voltage vs time\n",
    "plt.plot(data['time(s)'], data['current(A)'])\n",
    "plt.plot(data['time(s)'], data['potential(V)'])\n",
    "\n",
    "plt.show()"
   ]
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   "source": [
    "mean_current = data[\"current(A)\"].mean()\n",
    "mean_potential = data[\"potential(V)\"].mean()\n",
    "\n",
    "print('Mean current = {0} A;  Mean potential = {1} V'.format(mean_current, mean_potential))"
   ]
  },
  {
   "cell_type": "markdown",
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   },
   "source": [
    "# Tips and tricks (keyboard shortcuts and %magic)"
   ]
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   "source": [
    "# Keyboard shortcuts\n",
    "### Command mode vs. Edit mode\n",
    "\n",
    "Toggle with `esc` and `enter` keys\n",
    "\n",
    "### Useful command mode shortcuts\n",
    "|Command|Action|\n",
    "|:-----:|:----:|\n",
    "|a|Create new cell above|\n",
    "|b|Create new cell below|\n",
    "|d d|Delete current cell|\n",
    "|z| Undo delete cell|\n",
    "|m|Change cell to markdown|\n",
    "|y|Change cell to code|\n",
    "|h| Bring up the list of shortcuts|\n",
    "\n",
    "### Useful editing shortcuts\n",
    "\n",
    "|Command|Action|\n",
    "|:-----:|:----:|\n",
    "|Ctrl-a|Select all|\n",
    "|Ctrl-c|Copy|\n",
    "|Ctrl-v|Paste|\n",
    "|Ctrl-s|Save|\n",
    "|Tab| Autocomplete |\n",
    "|Shift-tab| Tooltips|"
   ]
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   "source": [
    "# %magics!\n",
    "\n",
    "Commands that add additional (usually more advanced) features to the notebook\n",
    "\n",
    "|Magic|Action|\n",
    "|:-----:|:----:|\n",
    "| %lsmagic | List all magics |\n",
    "| ! | Execute shell script |\n",
    "| %who(s) | See list of variables in current kernel |\n",
    "| %time(it)| Time a python expression <br>(w/ control over number of executions, etc.)|\n",
    "\n",
    "Many more built-in magic functions: http://ipython.readthedocs.io/en/stable/interactive/magics.html\n",
    "\n",
    "### Cell magics (%%) vs. line magics (%)\n",
    "\n",
    "Some magics have versions that apply to the entire cell by placing %%magic as the first line in a cell (i.e. %%timeit)"
   ]
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   "source": [
    "%timeit \",\".join(str(n) for n in range(100))"
   ]
  },
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   "metadata": {},
   "source": [
    "# Other cool stuff \n",
    "\n",
    "### Slideshow:\n",
    "\n",
    "    jupyter nbconvert notebook.ipynb --to slides --post serve\n",
    "    \n",
    "#### Online rendering with nbviewer: https://nbviewer.jupyter.org/\n",
    "\n",
    "#### Online execution with Binder: http://mybinder.org/"
   ]
  },
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