notes/Introduction_to_Markdown.ipynb

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    "Adapted from a notebook used in [BMS353 - Introduction to Bioinformatics](http://opendsi.cc/bioinformatics/)\n",
    "\n",
    "# Using the Jupyter Notebook as a Word Processor\n",
    "\n",
    "In this notebook we will list a set of basic formatting commands that helps when using markdown cells as Word processor.\n",
    "\n",
    "To see the Markdown source code of this cell, double click on it.\n",
    "\n",
    "\n",
    "## Markdown\n",
    "\n",
    "It is possible to use the notebook as a wordprocessor by making use of **Markdown Cells**. \n",
    "\n",
    "Markdown is a very simple language that allows you to format your text in your notebook. It is used in many research projects around the world and it represents an ideal tool for data sharing. As well as the Jupyter notebook, another very important project that uses Markdown to format text is the [github](https://github.com/) code-sharing site. SageMathCloud also makes use of github for code development.\n",
    "\n",
    "Markdown, being a language, has its own syntax to implement text formatting. In this brief document we list some commonly used syntax for basic text formatting.\n",
    "\n",
    "\n",
    "## Bold and italics\n",
    "\n",
    "Unlike word processors such as Microsoft Word, you do not highlight text and click on something to change its format. Instead, you use the Markdown syntax to tell the computer how to format your text.\n",
    "\n",
    "If you want some text to appear in bold, you surround it with two asterisks like this:\n",
    "\n",
    "    **This will be bold**\n",
    "\n",
    "the result format will be:\n",
    "\n",
    "**This will be bold**\n",
    "\n",
    "\n",
    "If you want the text to be in italics, you surround it in just one asterisk\n",
    "\n",
    "    *This will be in italics*\n",
    "\n",
    "\n",
    "the result format will be:\n",
    "\n",
    "*This will be in italics*\n",
    "\n",
    "## Lists\n",
    "\n",
    "We often create lists in our text, as bullet points or as numbered items.\n",
    "\n",
    "\n",
    "If we want to create bullet point lists, we can do so in markdown by putting an asterisk and a space in front of each item like this:\n",
    "\n",
    "    * item1\n",
    "    * item2\n",
    "    * item3\n",
    "\n",
    "\n",
    "the resulting format will be:\n",
    "\n",
    "\n",
    "* item1\n",
    "* item2\n",
    "* item3\n",
    "\n",
    "\n",
    "\n",
    "To create nested lists add 4 spaces to the beginning of each line to indent it by one level. Add 8 spaces to indent by two levels like in the example below:\n",
    "\n",
    "    * item1\n",
    "        * item1a\n",
    "        * item1b\n",
    "            * This has 8 spaces before the *\n",
    "    * item2\n",
    "\n",
    "\n",
    "the resulting format will be:\n",
    "\n",
    "\n",
    "* item1\n",
    "    * item1a - This has 4 spaces before the *\n",
    "    * item1b\n",
    "        * This has 8 spaces before the *\n",
    "* item2\n",
    "\n",
    "\n",
    "Finally to create a numbered list, you need to number the first entry and use asterisks for the other entries. \n",
    "\n",
    "    1. First\n",
    "    * Second\n",
    "    * Third\n",
    "\n",
    "1. First\n",
    "* Second\n",
    "* Third\n",
    "\n",
    "\n",
    "Markdown does not support numbered nested lists. If you want to create nested indented lists, you can use the 4 spaces indentation and numbered list, like in the example below:\n",
    "\n",
    "    1. Dog\n",
    "        * German Shepherd\n",
    "        * Belgian Shepherd\n",
    "            * Malinois\n",
    "            * Groenendael\n",
    "            * Tervuren\n",
    "    * Cat\n",
    "        * Siberian\n",
    "        * Siamese\n",
    "\n",
    "\n",
    "The result of the formatting is:    \n",
    "\n",
    "1. Dog\n",
    "    * German Shepherd\n",
    "    * Belgian Shepherd\n",
    "        * Malinois\n",
    "        * Groenendael\n",
    "        * Tervuren\n",
    "2. Cat\n",
    "    * Siberian\n",
    "    * Siamese\n",
    "\n",
    "\n",
    "\n",
    "## Mathematics\n",
    "\n",
    "You can also use mathematical notation in markdown. Within a markdown cell, something surrounded in `$` or `$$`, is considered as an equation. You write equations using a language called [$\\LaTeX$](http://www.latex-project.org/) (pronounced 'lay-tek' since the X is really a Greek letter chi). \n",
    "\n",
    "Don't worry, you don't need to learn very much of this language - most people only need to learn a tiny number of commands. Here are some examples:\n",
    "\n",
    "#### Superscript\n",
    "\n",
    "Commonly used for powers. You use the `^` symbol\n",
    "\n",
    "    $x^2$\n",
    "\n",
    "$x^2$\n",
    "\n",
    "#### Subscript\n",
    "\n",
    "One use for subscipts is in chemical forumlae:\n",
    "\n",
    "    $H_2O$\n",
    "\n",
    "$H_2O$\n",
    "\n",
    "\n",
    "#### Fractions\n",
    "\n",
    "Fractions are a little more complicated. We use the form `\\frac{numerator}{denominator}`\n",
    "\n",
    "    $\\frac{1}{x^2+1}$\n",
    "    \n",
    "$\\frac{1}{x^2+1}$\n",
    "\n",
    "\n",
    "`\\frac` is a $\\LaTeX$ command and all such commands start with a `\\`\n",
    "\n",
    "### Square root\n",
    "\n",
    "We need another $\\LaTeX$ command `\\sqrt`. The argument to the square root function is put in curly brackets\n",
    "\n",
    "    $\\sqrt{a+b}$\n",
    "    \n",
    "$\\sqrt{a+b}$\n",
    "\n",
    "\n",
    "### Sums\n",
    "\n",
    "To sum a quantity N times we can use \n",
    "\n",
    "    $\\sum_{n=1}^{N} 2^{-n} = 1$\n",
    "\n",
    "\n",
    "the result will be:\n",
    "\n",
    "$\\sum_{n=1}^{N} 2^{-n} = 1$\n",
    "\n",
    "\n",
    "\n",
    "### Products\n",
    "\n",
    "To multiply a quantity n times we can use \n",
    "\n",
    "    $\\prod_{i=a}^{b} f(i)$\n",
    "\n",
    "the results will be:\n",
    "\n",
    "$\\prod_{i=a}^{b} f(i)$\n",
    "\n",
    "### Integrals\n",
    "\n",
    "Integral notaton can be written using the following command:\n",
    "\n",
    "    $\\int_{a}^{b} x^2 dx$\n",
    "\n",
    "the result will be:\n",
    "\n",
    "$\\int_{a}^{b} x^2 dx$\n",
    "\n",
    "or we can use integral notation, without upper or lower limits, with the following command:\n",
    "\n",
    "    $\\int x^2 dx$\n",
    "    \n",
    "the result will be:\n",
    "\n",
    "$\\int x^2 dx$\n",
    "\n",
    "\n",
    "## Web links\n",
    "Web links such as http://www.walkingrandomly.com/ become clickable when the Markdown code is evaluated so just type them in.\n",
    "\n",
    "If you want to turn a piece of text into a weblink, you surround it in square brackets and put the web adress after it in round brackets. Like this:\n",
    "\n",
    "    [Here is a link to Mike's blog](http://www.walkingrandomly.com/)\n",
    "\n",
    "[Here is a link to Mike's blog](http://www.walkingrandomly.com/)\n",
    "\n",
    "\n",
    "\n",
    "## Images\n",
    "If the image is online, you use syntax that's very similar to a link but with a ! in front of it\n",
    "\n",
    "    ![The equation that says Hi](http://www.walkingrandomly.com/images/matlab/hi1_matlab.png)\n",
    "\n",
    "![The equation that says Hi](http://www.walkingrandomly.com/images/matlab/hi1_matlab.png)\n",
    "\n",
    "Alternatively, you can put an image in the same folder as your notebook and link to it like this:\n",
    "\n",
    "    ![Better Software Better Research](BetterSoftware_BetterResearch.jpg)\n",
    "    \n",
    "![Better Software Better Research](BetterSoftware_BetterResearch.jpg)\n",
    "\n",
    "\n",
    "## Tables\n",
    "\n",
    "You can create tables in Markdown cells by doing something like this:\n",
    "\n",
    "    Column A       | Column B\n",
    "    -------------  | -------------\n",
    "    Row 1          | 1.0\n",
    "    Row 2          | 2.0\n",
    "\n",
    "This produces the output\n",
    "\n",
    "Column A       | Column B\n",
    "-------------  | -------------\n",
    "Row 1          | 1.0\n",
    "Row 2          | 2.0\n",
    "\n",
    "In practice, you'll rarely do this as you'll generate your tables using the R programming language."
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