diff --git a/notebook.ipynb b/notebook.ipynb
index c75ebe0af11095e99bf3424f3fa0a0f846694073..84ad0542284c2fa26ddd5e0765afd1f74102cffa 100644
--- a/notebook.ipynb
+++ b/notebook.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:85ce76ec0467ad873d441ffde56b6f525d6e6d8f0e2be4d6ff89cea97f799b6e"
+ "signature": "sha256:bf6c651b1482834080a5bec22664d3f8b69e32fdf9036b00a12959d76f47d3be"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -18,7 +18,7 @@
"source": [
"<br></br><br></br>\n",
"\n",
- "\n",
+ "\n",
"\n",
"<br></br><br></br>"
]
@@ -38,63 +38,951 @@
"\n",
"[Sequencing Analysis Support Core, Leiden University Medical Center](http://sasc.lumc.nl)\n",
"\n",
- "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)\n",
+ "License:\n",
+ "\n",
+ "[Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)\n",
+ "\n",
+ "Examples and ideas taken from:\n",
+ "\n",
+ "1. http://nbviewer.ipython.org/github/ipython/ipython/blob/2.x/examples/Index.ipynb\n",
+ "\n",
+ "2. http://www.socrates.if.usp.br/~wtc/?q=role-computing-science\n",
"***"
]
},
{
- "cell_type": "markdown",
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Foreword: \n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 2,
+ "metadata": {},
+ "source": [
+ "Requirements on scientific computing"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "\"High-profile journals have called for increased openness in computational sciences. Some prestigious journals, including Science, have even started to demand of authors to provide the source code for simulation software used in publications to readers upon request.\""
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Reproducible Research in Computational Science, Roger D. Peng, Science 334, 1226 (2011).\n",
+ "- Shining Light into Black Boxes, A. Morin et al., Science 336, 159-160 (2012).\n",
+ "- The case for open computer programs, D.C. Ince, Nature 482, 485 (2012)."
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "The cornerstones of the scientific method:"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Replication\n",
+ "- Reproduction"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "To achieve this in scientific computing (programming):"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Any source code which generates data should be:\n",
+ " - Tracked!\n",
+ " - Backed up and secured\n",
+ " - Ideally published online\n",
+ " - Additionally: Also track external software versions and settings\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Revision Control System\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Systems such as \n",
+ " - Git\n",
+ " - SVN\n",
+ " \n",
+ " \n",
+ " \n",
+ "- Online repository\n",
+ " - Github"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Check out our one day Git course:"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "[Git course @ LUMC HumGen](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/gitcourse)"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Python in scientific computing"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Large community of users\n",
+ "- Extensive ecosystem of scientific libraries and environments\n",
+ "- Parallel processing with processes and threads\n",
+ "- Interprocess communication (MPI)\n",
+ "- GPU computing (OpenCL and CUDA)\n",
+ "- Readily available and suitable for use on high-performance computing clusters.\n",
+ "- No license costs, no unnecessary use of research budget."
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Strong position!"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "The python interpreter"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Standard way of running code\n",
+ "- Reads and runs the code in a file\n",
+ "\n",
+ "$ python my-program.py"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Alternatively, start the interpreter interactively by simply typing python\n",
+ "- Not very convenient due to a number of limitations\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "$ python"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ ""
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "IPython (Interactive Python)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Interactive shell with improved user friendliness"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ ""
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Command history\n",
+ "- Tab auto-completion\n",
+ "- In-line editing of code\n",
+ "- Object introspection, and automatic extract of documentation strings\n",
+ "- Good interaction with operating system shell\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "IPython Notebook"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "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"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ ""
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "IPython Notebook"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Cell based executable workflow\n",
+ "- Interactive computational documents\n",
+ "- Add elegant explanatory text\n",
+ "- Direct output of computations\n",
+ "- Add figures and video\n",
+ "- Integration in Git"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Why Notebook?"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "\"Web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document.\""
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "\"It is based on the IPython shell, but provides a cell-based environment with great interactivity, where calculations can be organized documented in a structured way.\""
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 3,
+ "metadata": {},
+ "source": [
+ "<br></br><br></br><br></br><br></br>\n",
+ "<font color='darkgreen'>Track, store and share elegant code using IPython Notebooks & Git!</font>\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 3,
+ "metadata": {},
+ "source": [
+ "<font color='darkgreen'>Replicability & Reproducibility</font>\n",
+ "<br></br><br></br><br></br><br></br>"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Getting started with IPython Notebook"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Where to Notebook?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Install locally\n",
+ " - See instructions in this course\n",
+ " \n",
+ " \n",
+ "- Shark cluster LUMC\n",
+ " - Type 'notebook' and click the URL"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "The user interface"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Cell based workflow\n",
+ "- Move between cells with the arrow keys or clicks with the mouse"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "There are two different modes from which always one is active"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Edit mode\n",
+ " - Hit ENTER or click the edit area to change to edit mode\n",
+ " - Indicated with a <font color='green'>green</font> cell border\n",
+ " - Edit your cell as if a normal text editor\n",
+ " \n",
+ "\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Command mode\n",
+ " - Hit ESCAPE to change into command mode\n",
+ " - 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",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "For example. Press 'b' to add a cell below in command mode to add a cell"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "a = 12"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 63
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "The toolbar is clickable"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ ""
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Edit mode shortcuts"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "\n",
+ "\n",
+ "- esc : command mode\n",
+ "- ctrl+m : command mode\n",
+ "- shift+enter : run cell\n",
+ "- ctrl+enter : run cell, select below\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Command mode shortcuts"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- enter : edit mode\n",
+ "- shift+enter : run cell\n",
+ "- ctrl+enter : run cell, select below\n",
+ "- y : to code\n",
+ "- m : to markdown\n",
+ "- ctrl+k : move cell up\n",
+ "- ctrl+j : move cell down\n",
+ "- a : insert cell above\n",
+ "- b : insert cell below\n",
+ "- x : cut cell\n",
+ "- c : copy cell\n",
+ "- v : paste cell below\n",
+ "- z : undo last delete\n",
+ "- d : delete cell (press twice)"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Two mayor cell types"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Code cell\n",
+ " - Contains code \n",
+ " - Inline comments\n",
+ " - Python or system calls\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# This is a code cell\n",
+ "x = 10"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [],
+ "prompt_number": 42
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Markdown cell\n",
+ " - Format your document nicely\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Set the cell type of the selected cell"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- Select the type from the dropdown box in the toolbar\n",
+ "- In command mode only: Press 'y' for code or 'm' for markdown"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Running code in a code cell"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Run a code cell by pressing the play button or shift+enter"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# Assign a value\n",
+ "a = 12\n",
+ "# Output a to the power of 3\n",
+ "print a**3"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "1728\n"
+ ]
+ }
+ ],
+ "prompt_number": 43
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "\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.\n",
+ " - Rename your notebook to something useful by clicking on the current name (Untitled1).\n",
+ "Add the code shown below to some cells and run it by pressing the play button or shift+enter"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "complements = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'} "
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "seq = 'GAATTC'"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "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": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "def reverse(s):\n",
+ " rev = s[::-1]\n",
+ " return rev"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "print reverse(translate(seq))"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Other uses of code cells\n"
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Except for code, some system aliases are available such as 'ls':"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "ls"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "biopython.ipynb \u001b[0m\u001b[01;34mimages\u001b[0m/ person.py \u001b[01;34msolutions\u001b[0m/\r\n",
+ "classes.ipynb INSTALL.md python.ipynb \u001b[01;34mstyles\u001b[0m/\r\n",
+ "\u001b[01;34mdata\u001b[0m/ matplotlib.ipynb README.md welcome.ipynb\r\n",
+ "\u001b[01;34mexamples\u001b[0m/ more-python.ipynb \u001b[01;32mseq_toolbox.py\u001b[0m*\r\n",
+ "exercises.ipynb Notebook.ipynb sequencer.ipynb\r\n",
+ "git.ipynb numpy.ipynb sequencer_old.py\r\n"
+ ]
+ }
+ ],
+ "prompt_number": 69
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Any command line program can be run using '!' with string interpolation from Python variables:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "message = 'Some text'\n",
+ "!echo $message"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "Some text\r\n"
+ ]
+ }
+ ],
+ "prompt_number": 70
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "!samtools"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "\r\n",
+ "Program: samtools (Tools for alignments in the SAM format)\r\n",
+ "Version: 0.1.19-44428cd\r\n",
+ "\r\n",
+ "Usage: samtools <command> [options]\r\n",
+ "\r\n",
+ "Command: view SAM<->BAM conversion\r\n",
+ " sort sort alignment file\r\n",
+ " mpileup multi-way pileup\r\n",
+ " depth compute the depth\r\n",
+ " faidx index/extract FASTA\r\n",
+ " tview text alignment viewer\r\n",
+ " index index alignment\r\n",
+ " idxstats BAM index stats (r595 or later)\r\n",
+ " fixmate fix mate information\r\n",
+ " flagstat simple stats\r\n",
+ " calmd recalculate MD/NM tags and '=' bases\r\n",
+ " merge merge sorted alignments\r\n",
+ " rmdup remove PCR duplicates\r\n",
+ " reheader replace BAM header\r\n",
+ " cat concatenate BAMs\r\n",
+ " bedcov read depth per BED region\r\n",
+ " targetcut cut fosmid regions (for fosmid pool only)\r\n",
+ " phase phase heterozygotes\r\n",
+ " bamshuf shuffle and group alignments by name\r\n",
+ "\r\n"
+ ]
+ }
+ ],
+ "prompt_number": 45
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Autocompletion works also by pressing TAB:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "import numpy\n",
+ "numpy.random.random()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 47,
+ "text": [
+ "0.7211185564561403"
+ ]
+ }
+ ],
+ "prompt_number": 47
+ },
+ {
+ "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,
+ "metadata": {},
+ "source": [
+ "Output from code cells"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "- 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",
+ " "
+ ]
+ },
+ {
+ "cell_type": "heading",
+ "level": 4,
+ "metadata": {},
+ "source": [
+ "Show some output and use it into another function"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "numpy.random.rand(3)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 86,
+ "text": [
+ "array([ 0.96757675, 0.54000181, 0.63633455])"
+ ]
+ }
+ ],
+ "prompt_number": 86
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "numpy.sin(_)\n"
+ ],
+ "language": "python",
"metadata": {},
- "source": [
- "# IPython Notebook"
- ]
+ "outputs": [
+ {
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 89,
+ "text": [
+ "array([ 0.73353825, 0.49178408, 0.55988864])"
+ ]
+ }
+ ],
+ "prompt_number": 89
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": [
- "Web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document."
+ "Scrollbars are automatically added for large outputs"
]
},
{
- "cell_type": "markdown",
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "for i in range(2):\n",
+ " print i"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": [
+ {
+ "output_type": "stream",
+ "stream": "stdout",
+ "text": [
+ "0\n",
+ "1\n"
+ ]
+ }
+ ],
+ "prompt_number": 115
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
"metadata": {},
"source": [
- "## Why Notebook?"
+ "Markdown cells"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "- Cell based executabel workflow\n",
- "- Interactive computational documents\n",
- "- Explanatory text\n",
- "- Results of computations\n",
- "- Figures and video\n"
+ "Formatted **text** _can_ **_be_** ~~aded~~ added to IPython Notebooks using Markdown cells. \n",
+ "\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Where to Notebook?"
+ "- Markdown is a popular markup language that is a superset of HTML. \n",
+ "- Its specification can be found here:\n",
+ " "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "- Install locally\n",
- "- Shark cluster LUMC"
+ "http://daringfireball.net/projects/markdown/"
]
},
{
- "cell_type": "markdown",
+ "cell_type": "heading",
+ "level": 1,
"metadata": {},
"source": [
- "# User interface"
+ "Some markdown examples: "
]
},
{
@@ -102,35 +990,25 @@
"level": 4,
"metadata": {},
"source": [
- "Move between cells with the arrow keys or clicks with the mouse"
+ "Headers can be put by using hashes '#'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "- Edit mode\n",
- " - Hit ENTER or click the edit area to change to edit mode\n",
- " - Indicated with a <font color='green'>green</font> cell border\n",
- " - Edit your cell as if a normal text editor\n",
- " \n",
- "\n",
- "\n",
- "\n"
+ "# Header 1\n",
+ "## Header 2\n",
+ "### Header 3"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "- Command mode\n",
- " - Hit ESCAPE to change into command mode\n",
- " - 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",
- "\n",
- "\n"
+ "# Header 1\n",
+ "## Header 2\n",
+ "### Header 3"
]
},
{
@@ -138,71 +1016,71 @@
"level": 4,
"metadata": {},
"source": [
- "Hit 'b' to add a cell below in command mode"
+ "Lists"
]
},
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "a = 12"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 63
- },
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Edit mode shortcuts"
+ "- A list\n",
+ " - A sublist\n",
+ " - Yet another level\n",
+ " - And so on"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "\n",
- "\n",
- "- esc : command mode\n",
- "- ctrl+m : command mode\n",
- "- shift+enter : run cell\n",
- "- ctrl+enter : run cell, select below\n"
+ "- A list\n",
+ " - A sublist\n",
+ " - Yet another level\n",
+ " - And so on"
]
},
{
- "cell_type": "markdown",
+ "cell_type": "heading",
+ "level": 4,
"metadata": {},
"source": [
- "## Command mode shortcuts"
+ "General HTML"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "- enter : edit mode\n",
- "- shift+enter : run cell\n",
- "- ctrl+enter : run cell, select below\n",
- "- y : to code\n",
- "- m : to markdown\n",
- "- ctrl+k : move cell up\n",
- "- ctrl+j : move cell down\n",
- "- a : insert cell above\n",
- "- b : insert cell below\n",
- "- x : cut cell\n",
- "- c : copy cell\n",
- "- v : paste cell below\n",
- "- z : undo last delete\n",
- "- d : delete cell (press twice)"
+ "<table border=\"1\" style=\"width:200px\">\n",
+ "<tr>\n",
+ " <td>Jill</td>\n",
+ " <td>Smith</td> \n",
+ " <td>50</td>\n",
+ "</tr>\n",
+ "<tr>\n",
+ " <td>Eve</td>\n",
+ " <td>Jackson</td> \n",
+ " <td>94</td>\n",
+ "</tr>\n",
+ "</table>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Running Code"
+ "<table border=\"1\" style=\"width:200px\">\n",
+ "<tr>\n",
+ " <td>Jill</td>\n",
+ " <td>Smith</td> \n",
+ " <td>50</td>\n",
+ "</tr>\n",
+ "<tr>\n",
+ " <td>Eve</td>\n",
+ " <td>Jackson</td> \n",
+ " <td>94</td>\n",
+ "</tr>\n",
+ "</table>"
]
},
{
@@ -210,769 +1088,283 @@
"level": 4,
"metadata": {},
"source": [
- "Run a code cell by pressing the play button or shift+enter"
+ "Markdown also supports formulas"
]
},
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "a =12"
- ],
- "language": "python",
+ "cell_type": "markdown",
"metadata": {},
- "outputs": [],
- "prompt_number": 64
+ "source": [
+ "\\begin{equation*} \\left( \\sum_{k=1}^n a_k b_k \\right)^2 \\leq \\left( \\sum_{k=1}^n a_k^2 \\right) \\left( \\sum_{k=1}^n b_k^2 \\right) \\end{equation*}\n"
+ ]
},
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print a"
- ],
- "language": "python",
+ "cell_type": "markdown",
"metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "12\n"
- ]
- }
- ],
- "prompt_number": 65
+ "source": [
+ "\\begin{equation*} \\left( \\sum_{k=1}^n a_k b_k \\right)^2 \\leq \\left( \\sum_{k=1}^n a_k^2 \\right) \\left( \\sum_{k=1}^n b_k^2 \\right) \\end{equation*}\n"
+ ]
},
{
"cell_type": "heading",
- "level": 4,
+ "level": 1,
"metadata": {},
"source": [
- "Some system aliases are available such as 'ls':"
+ "Plotting with matplotlib"
]
},
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "ls"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "biopython.ipynb \u001b[0m\u001b[01;34mimages\u001b[0m/ person.py \u001b[01;34msolutions\u001b[0m/\r\n",
- "classes.ipynb INSTALL.md python.ipynb \u001b[01;34mstyles\u001b[0m/\r\n",
- "\u001b[01;34mdata\u001b[0m/ matplotlib.ipynb README.md welcome.ipynb\r\n",
- "\u001b[01;34mexamples\u001b[0m/ more-python.ipynb \u001b[01;32mseq_toolbox.py\u001b[0m*\r\n",
- "exercises.ipynb Notebook.ipynb sequencer.ipynb\r\n",
- "git.ipynb numpy.ipynb sequencer_old.py\r\n"
- ]
- }
- ],
- "prompt_number": 69
- },
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": [
- "Any command line program can be run using '!' with string interpolation from Python variables:"
+ "More on this later in the course"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "message = 'Some text'\n",
- "!echo $message"
+ "%matplotlib inline\n",
+ "import matplotlib.pyplot as plt\n",
+ "plt.plot([x**2 for x in range(100)])\n",
+ "plt.show()"
],
"language": "python",
"metadata": {},
"outputs": [
{
- "output_type": "stream",
- "stream": "stdout",
+ "metadata": {},
+ "output_type": "display_data",
+ "png": 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xL05Vsb+TBwsd45drcSwn+91PeF28nhwysU7ZAjU4Ovv5QUksMQzHmpXAvhFc\n4OxXwT44E9mNQBvgOyAVuA27Hn67DmD//7dgE1SCdUw3Arbhv2txNTAf2AnkAuOwpmg/XosCx/ub\nKPxZWt0pOy6vJ4clQF1CN8h1ItQZ6QdJwGBsRMpbYeUTsI43nMc0EtsL2H/s2kBn4HPgIfx3HcA+\n+H4A6jnPm2GjdSbiv2uxGms3Pxv7W2mG/a348VoUON7fxATsb6cU9ndUF1hU7NHFmJ9vkGuCtbEv\nx5pUlmFDeytgnbOJPlTvWJoS+oLg1+vQAKs5rMC+LZfDv9fiWUJDWYdiNW2/XItUrK8lG/vC8AdO\n/Lu/gH2OrgZaFGukIiIiIiIiIiIiIiIiIiIiIiIiIiIiIiIiIiIisfT/aY4DA839B3AAAAAASUVO\nRK5CYII=\n",
"text": [
- "Some text\r\n"
+ "<matplotlib.figure.Figure at 0x3cda910>"
]
}
],
- "prompt_number": 70
+ "prompt_number": 21
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": [
- "Autocompletion work by pressing TAB:"
+ "Support for Latex"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "import numpy"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 71
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "numpy.random.random()"
+ "from IPython.display import Math\n",
+ "Math(r'F(k) = \\int_{-\\infty}^{\\infty} f(x) e^{2\\pi i k} dx')\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
+ "latex": [
+ "$$F(k) = \\int_{-\\infty}^{\\infty} f(x) e^{2\\pi i k} dx$$"
+ ],
"metadata": {},
"output_type": "pyout",
- "prompt_number": 72,
+ "prompt_number": 126,
"text": [
- "0.21343309815617817"
+ "<IPython.core.display.Math at 0x3318ed0>"
]
}
],
- "prompt_number": 72
+ "prompt_number": 126
+ },
+ {
+ "cell_type": "heading",
+ "level": 1,
+ "metadata": {},
+ "source": [
+ "Other integration such as videos"
+ ]
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": [
- "Exceptions are formatted nicely:"
+ "For example youtube"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "1/0"
+ "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": [
{
- "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-73-05c9758a9c21>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;36m1\u001b[0m\u001b[1;33m/\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[1;31mZeroDivisionError\u001b[0m: integer division or modulo by zero"
+ "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,
+ "text": [
+ "<IPython.lib.display.YouTubeVideo at 0x331a6d0>"
]
}
],
- "prompt_number": 73
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Output"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "- 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",
- " "
- ]
+ "prompt_number": 116
},
{
"cell_type": "heading",
"level": 4,
"metadata": {},
"source": [
- "Show some output and use it into another function"
+ "<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"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "numpy.random.rand(3)"
+ "from IPython.core.display import HTML\n",
+ "def custom_style():\n",
+ " style = open('styles/notebook.css', 'r').read()\n",
+ " return HTML('<style>' + style + '</style>')\n",
+ "def custom_script():\n",
+ " script = open('styles/notebook.js', 'r').read()\n",
+ " return HTML('<script>' + script + '</script>')"
],
"language": "python",
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 86,
- "text": [
- "array([ 0.96757675, 0.54000181, 0.63633455])"
- ]
- }
- ],
- "prompt_number": 86
+ "outputs": [],
+ "prompt_number": 132
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "numpy.sin(_)\n"
+ "custom_style()"
],
"language": "python",
"metadata": {},
"outputs": [
{
+ "html": [
+ "<style>/*\n",
+ " https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers\n",
+ "*/\n",
+ "@font-face {\n",
+ " font-family: \"Computer Modern\";\n",
+ " src: url('http://mirrors.ctan.org/fonts/cm-unicode/fonts/otf/cmunss.otf');\n",
+ "}\n",
+ "div.cell{\n",
+ " width:800px;\n",
+ " margin-left:16% !important;\n",
+ " margin-right:auto;\n",
+ "}\n",
+ "h1 {\n",
+ " font-family: Helvetica, serif;\n",
+ "}\n",
+ "h4{\n",
+ " margin-top:12px;\n",
+ " margin-bottom: 3px;\n",
+ " }\n",
+ "div.text_cell_render{\n",
+ " font-family: Computer Modern, \"Helvetica Neue\", Arial, Helvetica, Geneva, sans-serif;\n",
+ " line-height: 145%;\n",
+ " font-size: 130%;\n",
+ " width:800px;\n",
+ " margin-left:auto;\n",
+ " margin-right:auto;\n",
+ "}\n",
+ ".CodeMirror{\n",
+ " font-family: \"Source Code Pro\", source-code-pro,Consolas, monospace;\n",
+ "}\n",
+ ".prompt{\n",
+ " display: None;\n",
+ "}\n",
+ ".text_cell_render .exercise {\n",
+ " font-weight: 300;\n",
+ " /*font-size: 22pt;*/\n",
+ " color: #4057A1;\n",
+ " font-style: italic;\n",
+ " /*margin-bottom: .5em;\n",
+ " margin-top: 0.5em;\n",
+ " display: block;*/\n",
+ "}\n",
+ ".text_cell_render .example {\n",
+ " font-weight: 300;\n",
+ " color: #40A157;\n",
+ " font-style: italic;\n",
+ "}\n",
+ "\n",
+ ".warning{\n",
+ " color: rgb( 240, 20, 20 )\n",
+ "}\n",
+ "</style>"
+ ],
"metadata": {},
"output_type": "pyout",
- "prompt_number": 89,
+ "prompt_number": 133,
"text": [
- "array([ 0.73353825, 0.49178408, 0.55988864])"
+ "<IPython.core.display.HTML at 0x3318850>"
]
}
],
- "prompt_number": 89
- },
- {
- "cell_type": "heading",
- "level": 4,
- "metadata": {},
- "source": [
- "Scrollbars are automatically added for large outputs"
- ]
+ "prompt_number": 133
},
{
"cell_type": "code",
"collapsed": false,
"input": [
- "for i in range(500):\n",
- " print i"
+ "custom_script()"
],
"language": "python",
"metadata": {},
"outputs": [
{
- "output_type": "stream",
- "stream": "stdout",
+ "html": [
+ "<script>// https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers\n",
+ "MathJax.Hub.Config({\n",
+ " TeX: {\n",
+ " extensions: [\"AMSmath.js\"]\n",
+ " },\n",
+ " tex2jax: {\n",
+ " inlineMath: [ ['$','$'], [\"\\\\(\",\"\\\\)\"] ],\n",
+ " displayMath: [ ['$$','$$'], [\"\\\\[\",\"\\\\]\"] ]\n",
+ " },\n",
+ " displayAlign: 'center', // Change this to 'center' to center equations.\n",
+ " \"HTML-CSS\": {\n",
+ " styles: {'.MathJax_Display': {\"margin\": 4}}\n",
+ " }\n",
+ " });\n",
+ "</script>"
+ ],
+ "metadata": {},
+ "output_type": "pyout",
+ "prompt_number": 134,
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+ "<IPython.core.display.HTML at 0x3318050>"
]
}
],
- "prompt_number": 91
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [],
- "language": "python",
- "metadata": {},
- "outputs": []
+ "prompt_number": 134
}
],
"metadata": {}