diff --git a/notebook.ipynb b/notebook.ipynb
index ff7d920b6194c5f05814f776b048a798f34b4037..0cb4c87d901ec0f1b37b591f5fbb38db72be2574 100644
--- a/notebook.ipynb
+++ b/notebook.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:f32a4926b7461da7133e01bae5a7f9c6b580667534ff6f2af9832df26de9c88e"
+ "signature": "sha256:50f0011df38c64a61f87d0fd5e0bd41496c221072c1ed80168340a42e699384e"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -88,15 +88,14 @@
"level": 4,
"metadata": {},
"source": [
- "The cornerstones of the scientific method:"
+ "The cornerstone of the scientific method:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "- Replication\n",
- "- Reproduction"
+ "- Replication & Reproduction"
]
},
{
@@ -181,7 +180,15 @@
"level": 4,
"metadata": {},
"source": [
- "Strong position!"
+ "Lots of reasons to python!\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "How to python?"
]
},
{
@@ -271,7 +278,7 @@
"source": [
"- Started by typing 'ipython notebook' in the directory where you want to store notebooks\n",
"- Opens a new browser window with an index page where existing notebooks are shown\n",
- "- New notebooks can be created in that directory"
+ "- New notebooks can be created in that same directory"
]
},
{
@@ -364,11 +371,12 @@
"metadata": {},
"source": [
"- Install locally\n",
- " - See instructions in this course\n",
+ " - See instructions in this course\n",
+ " - Linux, Windows\n",
" \n",
" \n",
- "- Shark cluster LUMC\n",
- " - Type 'notebook' and click the URL"
+ "- Remotely, Shark cluster LUMC\n",
+ " - Type 'notebook' and click the given URL"
]
},
{
@@ -418,7 +426,7 @@
" - Indicated with a <font color='grey'>grey</font> cell border\n",
" - Edit the notebook as a whole\n",
"\n",
- "Different shortcuts apply in both modes!\n",
+ "Note: Different shortcuts apply in both modes!\n",
"\n",
"\n"
]
@@ -434,13 +442,10 @@
{
"cell_type": "code",
"collapsed": false,
- "input": [
- "a = 12"
- ],
+ "input": [],
"language": "python",
"metadata": {},
- "outputs": [],
- "prompt_number": 63
+ "outputs": []
},
{
"cell_type": "heading",
@@ -472,7 +477,6 @@
"\n",
"\n",
"- esc : command mode\n",
- "- ctrl+m : command mode\n",
"- shift+enter : run cell\n",
"- ctrl+enter : run cell, select below\n"
]
@@ -492,19 +496,61 @@
"- enter : edit mode\n",
"- shift+enter : run cell\n",
"- ctrl+enter : run cell, select below\n",
+ "\n",
+ "\n",
"- y : to code\n",
"- m : to markdown\n",
+ "\n",
+ "\n",
"- ctrl+k : move cell up\n",
"- ctrl+j : move cell down\n",
+ "\n",
+ "\n",
"- a : insert cell above\n",
"- b : insert cell below\n",
+ "\n",
+ "\n",
"- x : cut cell\n",
"- c : copy cell\n",
"- v : paste cell below\n",
+ "\n",
+ "\n",
"- z : undo last delete\n",
"- d : delete cell (press twice)"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Press 'h' to show the help."
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Saving your notebook\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- The notebook automatically saves\n",
+ "- You can manually click the 'save' icon or press CTRL+s"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "**Checkpoints**\n",
+ "\n",
+ "Currently only single checkpoints are stored, but multiple checkpoints will be enabled for future versions of IPython and Bookstore. "
+ ]
+ },
{
"cell_type": "heading",
"level": 1,
@@ -539,8 +585,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "- Markdown cell\n",
- " - Format your document nicely\n"
+ "This is a markdown cell which allows to format your document nicely and add context to code cells."
]
},
{
@@ -564,13 +609,29 @@
"level": 1,
"metadata": {},
"source": [
- "Running code in a code cell"
+ "Running python code"
]
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
+ "source": [
+ "All of the python goodness works!"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Cells run asynchronous\n",
+ "- Results are persistent\n",
+ "- Save time by running intensive code blocks only once"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
"source": [
"Run a code cell by pressing the play button or shift+enter"
]
@@ -595,69 +656,23 @@
]
}
],
- "prompt_number": 43
+ "prompt_number": 10
},
{
- "cell_type": "heading",
- "level": 1,
+ "cell_type": "markdown",
"metadata": {},
"source": [
- "\u00a7 Excercise : My first Notebook"
+ "Use the 'Cell' option in the toolbar to run multiple cells at once."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "Start a Notebook session.\n",
- " - $ ipython notebook\n",
- "This opens a webbrowser and shows existing notebooks.\n",
- " - Create a new notebook by clicking the 'New notebook' button.\n",
- "A new tab will open with a fresh notebook. Rename your notebook to something useful\n",
- " - Click on the current name (Untitled1) and edit this\n",
- "Add the code shown below to some cells\n",
- " - Add cells by pressen the '+' button or ALT+ENTER"
+ "- If the kernel is busy running it states 'Busy' in the header of the window or tab\n",
+ "- The indicator in the top right corner shows the kernel state"
]
},
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "complements = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'} "
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "def translate(s):\n",
- " c = ''\n",
- " for i in s:\n",
- " c = c + complements[i]\n",
- " return c"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 3
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "def reverse(s):\n",
- " rev = s[::-1]\n",
- " return rev"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 7
- },
{
"cell_type": "heading",
"level": 1,
@@ -801,37 +816,65 @@
},
{
"cell_type": "heading",
- "level": 4,
+ "level": 1,
"metadata": {},
"source": [
- "Exceptions are formatted nicely:"
+ "\u00a7 Excercise : My first Notebook"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Start a Notebook session.\n",
+ " - $ ipython notebook\n",
+ "This opens a webbrowser and shows existing notebooks.\n",
+ " - Create a new notebook by clicking the 'New notebook' button.\n",
+ "A new tab will open with a fresh notebook. Rename your notebook to something useful\n",
+ " - Click on the current name (Untitled1) and edit this\n",
+ "Add the code shown below to some **_code_** cells\n",
+ " - Add cells by pressen the '+' button or ALT+ENTER\n",
+ " - Remember the keyboard shortcuts or the help function ('h')\n",
+ "\n",
+ "\n",
+ "Notice the laste cell produced output! We will continue to develop this notebook later this session."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "# Let's distribute a few cookies to nobody\n",
- "cookies = 3\n",
- "persons = 0\n",
- "share = cookies / persons\n",
- "print share"
+ "def translate(seq):\n",
+ " complements = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'}\n",
+ " c_seq = ''\n",
+ " for n in seq:\n",
+ " c_seq = c_seq + complements[n]\n",
+ " return c_seq"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 40
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "translate('ACGT')"
],
"language": "python",
"metadata": {},
"outputs": [
{
- "ename": "ZeroDivisionError",
- "evalue": "integer division or modulo by zero",
- "output_type": "pyerr",
- "traceback": [
- "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mZeroDivisionError\u001b[0m Traceback (most recent call last)",
- "\u001b[1;32m<ipython-input-51-0d805d7db48f>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 2\u001b[0m \u001b[0mcookies\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m3\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[0mpersons\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 4\u001b[1;33m \u001b[0mshare\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcookies\u001b[0m \u001b[1;33m/\u001b[0m \u001b[0mpersons\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 5\u001b[0m \u001b[1;32mprint\u001b[0m \u001b[0mshare\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
- "\u001b[1;31mZeroDivisionError\u001b[0m: integer division or modulo by zero"
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 41,
+ "text": [
+ "'TGCA'"
]
}
],
- "prompt_number": 51
+ "prompt_number": 41
},
{
"cell_type": "heading",
@@ -848,7 +891,7 @@
"- When a cell is run it can generate output\n",
"- This is shown below the cell in the output area\n",
"- Output is asynchronous\n",
- "- Outputs are objects and are available under the variable '_'\n",
+ "- Outputs are objects and the last one is available under the variable '_'\n",
" "
]
},
@@ -929,6 +972,40 @@
],
"prompt_number": 115
},
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Exceptions are formatted nicely:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# Let's distribute a few cookies to nobody\n",
+ "cookies = 3\n",
+ "persons = 0\n",
+ "share = cookies / persons\n",
+ "print share"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "ZeroDivisionError",
+ "evalue": "integer division or modulo by zero",
+ "output_type": "pyerr",
+ "traceback": [
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mZeroDivisionError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m<ipython-input-51-0d805d7db48f>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 2\u001b[0m \u001b[0mcookies\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m3\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[0mpersons\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 4\u001b[1;33m \u001b[0mshare\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcookies\u001b[0m \u001b[1;33m/\u001b[0m \u001b[0mpersons\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 5\u001b[0m \u001b[1;32mprint\u001b[0m \u001b[0mshare\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;31mZeroDivisionError\u001b[0m: integer division or modulo by zero"
+ ]
+ }
+ ],
+ "prompt_number": 51
+ },
{
"cell_type": "heading",
"level": 1,
@@ -941,7 +1018,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "Formatted **text** _can_ **_be_** ~~aded~~ added to IPython Notebooks using Markdown cells. \n",
+ "Formatted **text** _can_ **_be_** added to IPython Notebooks using Markdown cells. \n",
"\n"
]
},
@@ -961,6 +1038,17 @@
"http://daringfireball.net/projects/markdown/"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "To create a markdown cell:\n",
+ "- First focus on the cell you want to format\n",
+ "- Then select 'Markdown' the dropdown box in the toolbar or press 'm' in command mode\n",
+ "- Note that you need to run a markdown cell to show the result\n",
+ " - Click 'play' or SHIFT+ENTER"
+ ]
+ },
{
"cell_type": "heading",
"level": 1,
@@ -1037,6 +1125,13 @@
"General HTML"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Since markdown is a subset of HTML, this will also work"
+ ]
+ },
{
"cell_type": "raw",
"metadata": {},
@@ -1081,6 +1176,13 @@
"Markdown also supports formulas"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Nicely formatted"
+ ]
+ },
{
"cell_type": "raw",
"metadata": {},
@@ -1097,77 +1199,83 @@
},
{
"cell_type": "heading",
- "level": 1,
+ "level": 4,
"metadata": {},
"source": [
- "\u00a7 Excercise : My next Notebook"
+ "We can also show figures. These can be locally or linked from the www."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "Let's add some markdown cells\n",
- "- Select the top code cell, press ESC to go into command mode\n",
- "- Press 'b', this will add a cell above the selected cell\n",
- "- Notice the focus is on the new cell\n",
- "- Now press 'm' to set the celltype to Markdown\n",
- "- Press ENTER and add some text"
+ "- Notebook has acceess to all the files down in the directory"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "### My next notebook\n",
- "[Michiel van Galen](mailto:m.van_galen@lumc.nl)"
+ ""
]
},
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "complements = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'} "
- ],
- "language": "python",
+ "cell_type": "markdown",
"metadata": {},
- "outputs": [],
- "prompt_number": 8
+ "source": [
+ ""
+ ]
},
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "def translate(s):\n",
- " c = ''\n",
- " for i in s:\n",
- " c = c + complements[i]\n",
- " return c"
- ],
- "language": "python",
+ "cell_type": "heading",
+ "level": 1,
"metadata": {},
- "outputs": [],
- "prompt_number": 9
+ "source": [
+ "<br></br><br></br>\n",
+ "Some final examples:"
+ ]
},
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "def reverse(s):\n",
- " rev = s[::-1]\n",
- " return rev"
- ],
- "language": "python",
+ "cell_type": "heading",
+ "level": 4,
"metadata": {},
- "outputs": []
+ "source": [
+ "Python supports videos also. Note this is not a markdown cell, but a code cell using a python package."
+ ]
},
{
"cell_type": "code",
"collapsed": false,
- "input": [],
+ "input": [
+ "from IPython.display import YouTubeVideo\n",
+ "# a talk about IPython at Sage Days at U. Washington, Seattle.\n",
+ "# Video credit: William Stein.\n",
+ "YouTubeVideo('1j_HxD4iLn8')"
+ ],
"language": "python",
"metadata": {},
- "outputs": []
+ "outputs": [
+ {
+ "html": [
+ "\n",
+ " <iframe\n",
+ " width=\"400\"\n",
+ " height=300\"\n",
+ " src=\"https://www.youtube.com/embed/1j_HxD4iLn8\"\n",
+ " frameborder=\"0\"\n",
+ " allowfullscreen\n",
+ " ></iframe>\n",
+ " "
+ ],
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 34,
+ "text": [
+ "<IPython.lib.display.YouTubeVideo at 0x331c850>"
+ ]
+ }
+ ],
+ "prompt_number": 34
},
{
"cell_type": "heading",
@@ -1178,11 +1286,10 @@
]
},
{
- "cell_type": "heading",
- "level": 4,
+ "cell_type": "markdown",
"metadata": {},
"source": [
- "More on this later in the course"
+ "More on this later in the course."
]
},
{
@@ -1202,93 +1309,139 @@
"output_type": "display_data",
"png": 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"text": [
- "<matplotlib.figure.Figure at 0x3cda910>"
+ "<matplotlib.figure.Figure at 0x333b590>"
]
}
],
- "prompt_number": 21
+ "prompt_number": 36
},
{
"cell_type": "heading",
- "level": 4,
+ "level": 1,
"metadata": {},
"source": [
- "Support for Latex"
+ "\u00a7 Excercise : My first Notebook"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Let's add some markdown cells to the notebook you created earlier:\n",
+ " - Select the top code cell\n",
+ " - Press ESC to go into command mode\n",
+ " - Press 'b', this will add a cell above the selected cell\n",
+ " - Notice the focus is on the new cell\n",
+ " - Now press 'm' to set the celltype to Markdown\n",
+ " - Press ENTER and add some code (see below for example)\n",
+ " - Run the cell and see if it worked\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Example markdown code:"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### My next notebook\n",
+ "\n",
+ "This notebook is my first notebook with some experimental code.\n",
+ "\n",
+ "Author: [Michiel van Galen](mailto:m.van_galen@lumc.nl)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now, try to add more python code to the notebook:\n",
+ " - Make sure to set the cell type to code\n",
+ " - Add the 'reverse' function to your notebook as shown below"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "from IPython.display import Math\n",
- "Math(r'F(k) = \\int_{-\\infty}^{\\infty} f(x) e^{2\\pi i k} dx')\n"
+ "def reverse(seq):\n",
+ " rev = seq[::-1]\n",
+ " return rev"
],
"language": "python",
"metadata": {},
- "outputs": [
- {
- "latex": [
- "$$F(k) = \\int_{-\\infty}^{\\infty} f(x) e^{2\\pi i k} dx$$"
- ],
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 126,
- "text": [
- "<IPython.core.display.Math at 0x3318ed0>"
- ]
- }
- ],
- "prompt_number": 126
+ "outputs": [],
+ "prompt_number": 42
},
{
- "cell_type": "heading",
- "level": 1,
+ "cell_type": "markdown",
"metadata": {},
"source": [
- "Other integration such as videos"
+ "Try using both the 'reverse' and 'translate' function."
]
},
{
- "cell_type": "heading",
- "level": 4,
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "reverse('AACGT')"
+ ],
+ "language": "python",
"metadata": {},
- "source": [
- "For example youtube"
- ]
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 45,
+ "text": [
+ "'TGCAA'"
+ ]
+ }
+ ],
+ "prompt_number": 45
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "from IPython.display import YouTubeVideo\n",
- "# a talk about IPython at Sage Days at U. Washington, Seattle.\n",
- "# Video credit: William Stein.\n",
- "YouTubeVideo('1j_HxD4iLn8')"
+ "translate(_)"
],
"language": "python",
"metadata": {},
"outputs": [
{
- "html": [
- "\n",
- " <iframe\n",
- " width=\"400\"\n",
- " height=300\"\n",
- " src=\"https://www.youtube.com/embed/1j_HxD4iLn8\"\n",
- " frameborder=\"0\"\n",
- " allowfullscreen\n",
- " ></iframe>\n",
- " "
- ],
"metadata": {},
"output_type": "pyout",
- "prompt_number": 116,
+ "prompt_number": 46,
"text": [
- "<IPython.lib.display.YouTubeVideo at 0x331a6d0>"
+ "'ACGTT'"
]
}
],
- "prompt_number": 116
+ "prompt_number": 46
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Palindromic sequences play an important role in molecular biology:\n",
+ "\n",
+ "http://en.wikipedia.org/wiki/Palindromic_sequence"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Add the following features to your notebook:\n",
+ " - Think of function which can test if a seqeunce is palindromic\n",
+ " - Nicely formatted mardown cell(s) explaining the notebook\n",
+ " - Add links as references like above"
+ ]
},
{
"cell_type": "heading",
@@ -1299,6 +1452,7 @@
"<br></br><br></br><br></br><br></br>\n",
"<br></br><br></br><br></br><br></br>\n",
"<br></br><br></br><br></br><br></br>\n",
+ "<br></br><br></br><br></br><br></br>\n",
"Ignore following code for layout"
]
},