XMerge branch 'master' of git.lumc.nl:courses/programming-course

239762f2 · jkvis · 12fac270 · 3a94007d · 239762f2 · 239762f2
Commit 239762f2 authored 7 years ago by jkvis
--- a/README.md
+++ b/README.md
@@ -23,7 +23,7 @@ be done in your own time (i.e., during the afternoons).

 Please note that the above mentioned date and location are subject to change.

-Program
+Program and Materials
 -------

 - Mornings: presentations.
@@ -31,13 +31,13 @@ Program

 | Day             | Time  | Lesson                              | Teacher  | 
 |-----------------|-------|------------------------------------ |----------|
-| Monday, 18/9    | 9-10  | Welcome, Introduction to Python (1) | Mihai    | 
-|                 | 10-11 | Introduction to Python (2)          | Jeroen   |  
-|                 | 11-12 | Introduction to Python (3)          | Mihai    | 
+| Monday, 18/9    | 9-10  | [Welcome][lesson_01], [Introduction to Python (1)][lesson_02_01] | Mihai    | 
+|                 | 10-11 | [Introduction to Python (2)][lesson_02_02]          | Jeroen   |  
+|                 | 11-12 | [Introduction to Python (3)][lesson_02_03]          | Mihai    | 
 |                 | 12-13 | Practical help                      |          | 
 | Tuesday, 19/9   | 9-10  | Assignments review                  |          |
-|                 | 10-11 | More Python Goodness (1)            | Mihai    | 
-|                 | 11-12 | More Python Goodness (2)            | Mihai    | 
+|                 | 10-11 | [More Python Goodness (1)][lesson_03_01]            | Mihai    | 
+|                 | 11-12 | [More Python Goodness (2)][lesson_03_02]            | Mihai    | 
 |                 | 12-13 | IPython Notebook                    | Mark     | 
 | Wednesday, 20/9 | 9-10  | Assignments review                  |          | 
 |                 | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     | 
@@ -48,29 +48,22 @@ Program
 |                 | 11-12 | Biopython                           | Guy      | 
 |                 | 12-13 | Putting everything together         | Jeroen   |

+Some of the lessons are slideshows, whereas others are just
+notebooks we scroll through during class. The links above are all one-page
+static renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/).

-Materials
---------

-The top-level directory contains materials for the following lessons:
+Assignments
+-------
+- [First day](https://classroom.github.com/a/QU2iPYKn).

-1. Welcome ([slides][lesson_01])
-2. Introduction to Python ([slides 1][lesson_02_01], [slides 2][lesson_02_02],
-   [slides 3][lesson_02_03])
-3. More Python Goodness ([notebook 1][lesson_03_01], [notebook 2][lesson_03_02])
-4. Working with NumPy arrays ([slides][lesson_04])
-5. IPython Notebook ([notebook][lesson_05])
-6. Plotting with matplotlib ([notebook][lesson_06])
-7. Painting Pandas ([slides][lesson_07])
-8. Object-oriented programming ([slides][lesson_08])
-9. A sip of Biopython ([notebook 1][lesson_09_01], [notebook 2][lesson_09_02])

 [lesson_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/01_welcome.ipynb
-[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(1).ipynb
-[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(2).ipynb
-[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(3).ipynb
-[lesson_03_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(1).ipynb
-[lesson_03_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(2).ipynb
+[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/02_introduction_to_python_1.ipynb
+[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/02_introduction_to_python_2.ipynb
+[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/02_introduction_to_python_3.ipynb
+[lesson_03_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/more_python/03_more_python_goodness_1.ipynb
+[lesson_03_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/more_python/03_more_python_goodness_2.ipynb
 [lesson_04]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/04%20-%20Working%20with%20NumPy%20arrays.ipynb
 [lesson_05]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/05%20-%20IPython%20Notebook.ipynb
 [lesson_06]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/06%20-%20Plotting%20with%20matplotlib.ipynb
@@ -79,17 +72,10 @@ The top-level directory contains materials for the following lessons:
 [lesson_09_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(1).ipynb
 [lesson_09_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(2).ipynb

-As indicated, some of the lessons are slideshows, whereas others are just
-notebooks we scroll through during class. The links above are all one-page
-static renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/).
-
-We also have a
-[repository with material for the assignments](https://git.lumc.nl/courses/programming-course-assignments).
-
 Software installation
 ---------------------

-See the instructions in [INSTALL.md](/INSTALL.md).
+See the instructions [here](https://docs.anaconda.com/anaconda/install/).

 Notebooks
 ---------

--- a/images/python_logo.svg
+++ b/images/python_logo.svg
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   version="1.1"
+   viewBox="0 0 1052.4 368.09"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="python_logo.svg"
+   width="1052.4"
+   height="368.09003">
+  <metadata
+     id="metadata14">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <defs
+     id="defs12" />
+  <sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="2495"
+     inkscape:window-height="1416"
+     id="namedview10"
+     showgrid="false"
+     inkscape:zoom="0.8009039"
+     inkscape:cx="589.44223"
+     inkscape:cy="227.21656"
+     inkscape:window-x="65"
+     inkscape:window-y="24"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="svg2" />
+  <g
+     transform="translate(324.63321,-501.97596)"
+     id="g4">
+    <path
+       d="m 524.02,846.67 c -33.839,-1.2297 -54.784,-11.264 -60.113,-28.8 l -0.6194,-2.0382 -0.0869,-34.378 c -0.0994,-39.346 -0.0645,-40.143 2.0299,-46.408 3.8218,-11.432 12.859,-18.803 26.993,-22.016 l 3.1253,-0.71039 38.862,-0.17214 c 27.843,-0.12334 39.388,-0.26278 40.716,-0.49179 7.7818,-1.3418 12.887,-3.3508 17.679,-6.9578 5.7253,-4.309 10.451,-11.685 12.563,-19.607 1.5862,-5.9503 1.5436,-5.3002 1.715,-26.202 l 0.15935,-19.431 27.992,0 2.7176,0.75892 c 14.561,4.0662 25.133,17.862 29.633,38.671 1.7311,8.0037 1.7492,8.2998 1.7524,28.718 0.003,19.87 -0.006,20.044 -1.3943,26.562 -1.3645,6.4064 -3.1506,11.619 -5.8196,16.985 -5.3828,10.822 -13.32,18.146 -23.357,21.553 -5.7335,1.9464 -0.93423,1.7836 -57.342,1.9449 l -50.82,0.14528 0,9.24 33.699,0.13588 33.699,0.13589 0.13588,16.578 c 0.0747,9.1177 0.0421,17.36 -0.0725,18.316 -0.27725,2.3131 -1.2585,5.0581 -2.6625,7.4485 -1.4458,2.4616 -5.8352,6.8642 -8.8149,8.8417 -9.0505,6.0063 -22.849,9.6675 -41.036,10.888 -6.1192,0.41068 -14.785,0.52882 -21.333,0.29086 z m 46.743,-21.481 c 6.4954,-1.053 11.145,-7.4099 10.074,-13.773 -0.88336,-5.2488 -4.9357,-9.3086 -10.155,-10.173 -7.9672,-1.3202 -15.213,5.9958 -13.795,13.929 1.0313,5.7708 5.6585,9.8336 11.701,10.274 0.2242,0.0163 1.2026,-0.0992 2.1741,-0.25667 z m -144.8,-49.035 c -7.6439,-1.3898 -15.171,-6.0227 -20.491,-12.611 -10.075,-12.479 -15.162,-33.284 -14.523,-59.406 0.3979,-16.278 2.8315,-28.362 7.782,-38.641 6.3813,-13.25 15.916,-21.108 28.787,-23.724 2.8193,-0.57313 2.9606,-0.57462 52.615,-0.55479 27.384,0.0109 49.989,-0.0572 50.235,-0.1514 0.38956,-0.14949 0.44634,-0.75521 0.44634,-4.7622 0,-2.525 -0.0306,-4.6203 -0.0679,-4.6562 -0.0374,-0.0359 -15.232,-0.12763 -33.767,-0.20383 l -33.699,-0.13854 -0.07,-17.514 c -0.0766,-19.183 -0.092,-18.96 1.5503,-22.483 5.6933,-12.213 22.465,-19.633 49.339,-21.829 1.9431,-0.1588 7.2017,-0.36064 11.686,-0.44852 29.753,-0.58311 51.579,4.8575 63.052,15.717 1.271,1.2031 2.9273,2.9988 3.6807,3.9906 1.7132,2.255 3.8458,6.5603 4.6624,9.4125 l 0.62243,2.1741 0,36.145 c 0,33.739 -0.0327,36.316 -0.49158,38.726 -0.59212,3.1098 -2.0144,7.4792 -3.1997,9.8301 -4.1039,8.1393 -11.665,14.003 -21.689,16.82 -6.5086,1.8288 -3.5525,1.7086 -46.637,1.8956 -42.787,0.18564 -40.201,0.086 -46.2,1.7812 -11.651,3.2927 -20.21,12.367 -23.687,25.113 -1.5631,5.7299 -1.5284,5.1946 -1.6996,26.225 l -0.15925,19.567 -13.045,0.0447 c -9.8474,0.0338 -13.532,-0.0439 -15.034,-0.31707 z m 71.232,-162.58 c 4.9456,-2.3234 7.924,-7.7698 7.0286,-12.853 -0.82592,-4.6888 -4.0455,-8.4308 -8.4148,-9.7804 -6.983,-2.1568 -14.269,2.2939 -15.558,9.5032 -1.0478,5.8633 2.3432,11.571 8.0784,13.598 1.2817,0.45295 2.1059,0.54476 4.303,0.47938 2.3937,-0.0712 2.9375,-0.18417 4.5622,-0.94747 z"
+       id="path6"
+       inkscape:connector-curvature="0"
+       style="fill:#fed142" />
+    <path
+       d="m 425.96,776.15 c -7.6439,-1.3898 -15.171,-6.0227 -20.491,-12.611 -10.075,-12.479 -15.162,-33.284 -14.523,-59.406 0.3979,-16.278 2.8315,-28.362 7.782,-38.641 6.3813,-13.25 15.916,-21.108 28.787,-23.724 2.8193,-0.57313 2.9606,-0.57462 52.615,-0.55479 27.384,0.0109 49.989,-0.0572 50.235,-0.1514 0.38956,-0.14949 0.44634,-0.75521 0.44634,-4.7622 0,-2.525 -0.0306,-4.6203 -0.0679,-4.6562 -0.0374,-0.0359 -15.232,-0.12763 -33.767,-0.20383 l -33.699,-0.13854 -0.07,-17.514 c -0.0766,-19.183 -0.092,-18.96 1.5503,-22.483 5.6933,-12.213 22.465,-19.633 49.339,-21.829 1.9431,-0.1588 7.2017,-0.36064 11.686,-0.44852 29.753,-0.58311 51.579,4.8575 63.052,15.717 1.271,1.2031 2.9273,2.9988 3.6807,3.9906 1.7132,2.255 3.8458,6.5603 4.6624,9.4125 l 0.62243,2.1741 0,36.145 c 0,33.739 -0.0327,36.316 -0.49158,38.726 -0.59212,3.1098 -2.0144,7.4792 -3.1997,9.8301 -4.1039,8.1393 -11.665,14.003 -21.689,16.82 -6.5086,1.8288 -3.5525,1.7086 -46.637,1.8956 -42.787,0.18564 -40.201,0.086 -46.2,1.7812 -11.651,3.2927 -20.21,12.367 -23.687,25.113 -1.5631,5.7299 -1.5284,5.1946 -1.6996,26.225 l -0.15925,19.567 -13.045,0.0447 c -9.8474,0.0338 -13.532,-0.0439 -15.034,-0.31707 z m 71.232,-162.58 c 4.9456,-2.3234 7.924,-7.7698 7.0286,-12.853 -0.82592,-4.6888 -4.0455,-8.4308 -8.4148,-9.7804 -6.983,-2.1568 -14.269,2.2939 -15.558,9.5032 -1.0478,5.8633 2.3432,11.571 8.0784,13.598 1.2817,0.45295 2.1059,0.54476 4.303,0.47938 2.3937,-0.0712 2.9375,-0.18417 4.5622,-0.94747 z"
+       id="path8"
+       inkscape:connector-curvature="0"
+       style="fill:#3571a3" />
+  </g>
+</svg>
--- a/introduction/01_welcome.ipynb
+++ b/introduction/01_welcome.ipynb
@@ -11,8 +11,7 @@
    "<span style=\"font-size: 200%\">Programming in Python</span>\n",
    "===\n",
    "\n",
-    "<br>\n",
-    "\n"
+    "<br>"
   ]
  },
  {
@@ -27,12 +26,36 @@
    "===\n",
    "\n",
    "* Aimed at PhD students, Postdocs, researchers, analysts, ...\n",
-    "* Programming as a tool to do your research.\n",
-    "* Slightly focussed on bioinformatics.\n",
+    "* Focus on:\n",
+    " - Basic understanding of Python.\n",
+    " - Programming as a tool to do your research.\n",
+    "    - Slightly biased on bioinformatics.\n",
+    "\n",
    "\n",
    "**Note:** This is its third session."
   ]
  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "Hands on!\n",
+    "===\n",
+    "\n",
+    "**Programming is fun!**\n",
+    "* You only learn programming by doing it.\n",
+    "* Lecture format:\n",
+    "    - Blended teaching + exercising.\n",
+    "* Have your laptop open during the lessons.\n",
+    "* Repeat the code from the slides, play around with it.\n",
+    "* Do the session exercises.\n",
+    "* There will be a few assignments to submit."
+   ]
+  },
  {
   "cell_type": "markdown",
   "metadata": {
@@ -75,24 +98,37 @@
    "Program\n",
    "===\n",
    "\n",
-    "| Day             | Time  | Lesson                              | Teacher  | \n",
-    "|-----------------|-------|------------------------------------ |----------|\n",
-    "| Monday, 18/9    | 9-10  | Welcome, Introduction to Python (1) | Mihai    | \n",
-    "|                 | 10-11 | Introduction to Python (2)          | Jeroen   |  \n",
-    "|                 | 11-12 | Introduction to Python (3)          | Mihai    | \n",
-    "|                 | 12-13 | Practical help                      |          | \n",
-    "| Tuesday, 19/9   | 9-10  | Assignments review                  |          |\n",
-    "|                 | 10-11 | More Python Goodness (1)            | Mihai    | \n",
-    "|                 | 11-12 | More Python Goodness (2)            | Mihai    | \n",
-    "|                 | 12-13 | IPython Notebook                    | Mark     | \n",
-    "| Wednesday, 20/9 | 9-10  | Assignments review                  |          | \n",
-    "|                 | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     | \n",
-    "|                 | 11-12 | Data visualisation (1)              | Guy      | \n",
-    "|                 | 12-13 | Data visualisation (2)              | Guy      | \n",
-    "| Thursday, 21/9  | 9-10  | Assignments review                  |          | \n",
-    "|                 | 10-11 | Object-oriented programming         | Jonathan | \n",
-    "|                 | 11-12 | Biopython                           | Guy      | \n",
-    "|                 | 12-13 | Putting everything together         | Jeroen   |\n",
+    "| Day               | Time  | Lesson                              | Teacher  | \n",
+    "|-------------------|-------|------------------------------------ |----------|\n",
+    "| **Monday, 18/9**  | 9 - 9:30  | Welcome, Setup                  | Mihai    | \n",
+    "|                   | 9:30 - 10:30 |  Introduction to Python (1)  | Mihai    |\n",
+    "|                   | 10:30 - 11:30 | Introduction to Python (2)  | Jeroen   |  \n",
+    "|                   | 11:30 - 12:30 | Introduction to Python (3)  | Mihai    | \n",
+    "|                   | 12:30 - 13:00 | Practical help              |          | \n",
+    "| **Tuesday, 19/9** | 9-10  | Assignments review                  |          |\n",
+    "|                   | 10-11 | More Python Goodness (1)            | Mihai    | \n",
+    "|                   | 11-12 | More Python Goodness (2)            | Mihai    | \n",
+    "|                   | 12-13 | IPython Notebook                    | Mark     | "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
+   "source": [
+    "| Day                 | Time  | Lesson                              | Teacher  | \n",
+    "|---------------------|-------|------------------------------------ |----------|\n",
+    "| **Wednesday, 20/9** | 9-10  | Assignments review                  |          | \n",
+    "|                     | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     | \n",
+    "|                     | 11-12 | Data visualisation (1)              | Guy      | \n",
+    "|                     | 12-13 | Data visualisation (2)              | Guy      | \n",
+    "| **Thursday, 21/9**  | 9-10  | Assignments review                  |          | \n",
+    "|                     | 10-11 | Object-oriented programming         | Jonathan | \n",
+    "|                     | 11-12 | Biopython                           | Guy      | \n",
+    "|                     | 12-13 | Putting everything together         | Jeroen   |\n",
    "\n",
    "All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course)"
   ]
@@ -108,12 +144,15 @@
    "Software requirements\n",
    "===\n",
    "\n",
-    "* Anaconda\n",
-    "    * Python 2.7\n",
-    "    * NumPy, matplotlib, Biopython\n",
+    "* Anaconda:\n",
+    "  * Python 2.7\n",
+    "  * Comes with all that's required:\n",
+    "    - Python interpreter, Jupyter Notebook.\n",
+    "    - Libraries:\n",
+    "      - NumPy, Panda, matplotlib, Bokeh, Biopython, ...\n",
+    "  * [Installation instructions](https://docs.anaconda.com/anaconda/install/). \n",
    "* Git\n",
-    "\n",
-    "Anaconda installation instructions [here](https://docs.anaconda.com/anaconda/install/)."
+    "\n"
   ]
  },
  {
@@ -124,15 +163,17 @@
    }
   },
   "source": [
-    "Exercises\n",
+    "Assignments\n",
    "===\n",
    "\n",
-    "You only learn programming by doing it.\n",
-    "\n",
-    "* Have your laptop open during the lessons.\n",
-    "* Repeat the code from the slides, play around with it.\n",
-    "* Do the exercises.\n",
-    "* There will be a few assignments to submit."
+    "* We make use of GitHub Classroom.\n",
+    "* GitHub account required.\n",
+    "* Receive link with assignment repository.\n",
+    "* Own forked repository to work on.\n",
+    "  - Clone it.\n",
+    "  - Code.\n",
+    "  - Push it.\n",
+    "* Direct file upload to repository is also possible."
   ]
  },
  {
@@ -152,7 +193,7 @@
  },
  {
   "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
@@ -191,7 +232,7 @@
       "<IPython.core.display.HTML object>"
      ]
     },
-     "execution_count": 3,
+     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
@@ -208,7 +249,7 @@
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
-     "slide_type": "slide"
+     "slide_type": "-"
    }
   },
   "source": [
@@ -217,22 +258,23 @@
  }
 ],
 "metadata": {
+  "celltoolbar": "Slideshow",
  "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
   "language": "python",
-   "name": "python3"
+   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
-    "version": 3
+    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.12"
  }
 },
 "nbformat": 4,

 %% Cell type:markdown id: tags:

 <span style="font-size: 200%">Programming in Python</span>
 ===

 <br>

-
 %% Cell type:markdown id: tags:

 About the course
 ===

 * Aimed at PhD students, Postdocs, researchers, analysts, ...
-* Programming as a tool to do your research.
-* Slightly focussed on bioinformatics.
+* Focus on:
+ - Basic understanding of Python.
+ - Programming as a tool to do your research.
+    - Slightly biased on bioinformatics.
+

 **Note:** This is its third session.

 %% Cell type:markdown id: tags:

+Hands on!
+===
+
+**Programming is fun!**
+* You only learn programming by doing it.
+* Lecture format:
+    - Blended teaching + exercising.
+* Have your laptop open during the lessons.
+* Repeat the code from the slides, play around with it.
+* Do the session exercises.
+* There will be a few assignments to submit.
+
+%% Cell type:markdown id: tags:
+
 Teachers
 ===

 * Jeroen Laros<br>
  [j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl)


 * Mihai Lefter<br>
  [m.lefter@lumc.nl](mailto:m.lefter@lumc.nl)


 * Jonathan Vis<br>
  [j.k.vis@lumc.nl](mailto:j.k.vis@lumc.nl)


 * Mark Santcroos<br>
  [m.a.santcroos@lumc.nl](mailto:m.a.santcroos@lumc.nl)


 * Guy Allard<br>
  [w.g.Allard@lumc.nl](mailto:w.g.allard@lumc.nl)

 %% Cell type:markdown id: tags:

 Program
 ===

-| Day             | Time  | Lesson                              | Teacher  |
-|-----------------|-------|------------------------------------ |----------|
-| Monday, 18/9    | 9-10  | Welcome, Introduction to Python (1) | Mihai    |
-|                 | 10-11 | Introduction to Python (2)          | Jeroen   |
-|                 | 11-12 | Introduction to Python (3)          | Mihai    |
-|                 | 12-13 | Practical help                      |          |
-| Tuesday, 19/9   | 9-10  | Assignments review                  |          |
-|                 | 10-11 | More Python Goodness (1)            | Mihai    |
-|                 | 11-12 | More Python Goodness (2)            | Mihai    |
-|                 | 12-13 | IPython Notebook                    | Mark     |
-| Wednesday, 20/9 | 9-10  | Assignments review                  |          |
-|                 | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     |
-|                 | 11-12 | Data visualisation (1)              | Guy      |
-|                 | 12-13 | Data visualisation (2)              | Guy      |
-| Thursday, 21/9  | 9-10  | Assignments review                  |          |
-|                 | 10-11 | Object-oriented programming         | Jonathan |
-|                 | 11-12 | Biopython                           | Guy      |
-|                 | 12-13 | Putting everything together         | Jeroen   |
+| Day               | Time  | Lesson                              | Teacher  |
+|-------------------|-------|------------------------------------ |----------|
+| **Monday, 18/9**  | 9 - 9:30  | Welcome, Setup                  | Mihai    |
+|                   | 9:30 - 10:30 |  Introduction to Python (1)  | Mihai    |
+|                   | 10:30 - 11:30 | Introduction to Python (2)  | Jeroen   |
+|                   | 11:30 - 12:30 | Introduction to Python (3)  | Mihai    |
+|                   | 12:30 - 13:00 | Practical help              |          |
+| **Tuesday, 19/9** | 9-10  | Assignments review                  |          |
+|                   | 10-11 | More Python Goodness (1)            | Mihai    |
+|                   | 11-12 | More Python Goodness (2)            | Mihai    |
+|                   | 12-13 | IPython Notebook                    | Mark     |
+
+%% Cell type:markdown id: tags:
+
+| Day                 | Time  | Lesson                              | Teacher  |
+|---------------------|-------|------------------------------------ |----------|
+| **Wednesday, 20/9** | 9-10  | Assignments review                  |          |
+|                     | 10-11 | Data manipulation (NumPy, Pandas)   | Mark     |
+|                     | 11-12 | Data visualisation (1)              | Guy      |
+|                     | 12-13 | Data visualisation (2)              | Guy      |
+| **Thursday, 21/9**  | 9-10  | Assignments review                  |          |
+|                     | 10-11 | Object-oriented programming         | Jonathan |
+|                     | 11-12 | Biopython                           | Guy      |
+|                     | 12-13 | Putting everything together         | Jeroen   |

 All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course)

 %% Cell type:markdown id: tags:

 Software requirements
 ===

-* Anaconda
-    * Python 2.7
-    * NumPy, matplotlib, Biopython
+* Anaconda:
+  * Python 2.7
+  * Comes with all that's required:
+    - Python interpreter, Jupyter Notebook.
+    - Libraries:
+      - NumPy, Panda, matplotlib, Bokeh, Biopython, ...
+  * [Installation instructions](https://docs.anaconda.com/anaconda/install/).
 * Git

-Anaconda installation instructions [here](https://docs.anaconda.com/anaconda/install/).

 %% Cell type:markdown id: tags:

-Exercises
+Assignments
 ===

-You only learn programming by doing it.
-
-* Have your laptop open during the lessons.
-* Repeat the code from the slides, play around with it.
-* Do the exercises.
-* There will be a few assignments to submit.
+* We make use of GitHub Classroom.
+* GitHub account required.
+* Receive link with assignment repository.
+* Own forked repository to work on.
+  - Clone it.
+  - Code.
+  - Push it.
+* Direct file upload to repository is also possible.

 %% Cell type:markdown id: tags:

 Getting help
 ===

 * Ask a teacher.
 * If it's private, mail one of the teachers.

 %% Cell type:code id: tags:

 ``` python
 from IPython.display import HTML
 def css_styling():
    styles = open('../styles/custom.css', 'r').read()
    return HTML('<style>' + styles + '</style>')
 css_styling()
 ```

 %% Output

    <IPython.core.display.HTML object>

 %% Cell type:markdown id: tags:

 License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)

--- a/introduction/02_introduction_to_python_1.ipynb
+++ b/introduction/02_introduction_to_python_1.ipynb
@@ -9,17 +9,7 @@
   },
   "source": [
    "<span style=\"font-size: 200%\">Introduction to Python (1)</span>\n",
-    "===\n",
-    "\n",
-    "<br>\n",
-    "\n",
-    "[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
-    "\n",
-    "[Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
-    "\n",
-    "Based on: [Python Scientific Lecture Notes](http://scipy-lectures.github.io/)\n",
-    "\n",
-    "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
+    "===\n"
   ]
  },
  {
@@ -37,6 +27,7 @@
    "---\n",
    "\n",
    "* Created early 90's by Guido van Rossem at CWI.\n",
+    "  - Name: Monty Python.\n",
    "* General purpose, high-level programming language.\n",
    "* Design is driven by code readability."
   ]
@@ -56,7 +47,8 @@
    "---\n",
    "\n",
    "* Interpreted, no separate compilation step needed.\n",
-    "* Imperative and object-oriented programming (and some functional programming).\n",
+    "* Imperative and object-oriented programming.\n",
+    "  - And some functional programming.\n",
    "* Dynamic type system.\n",
    "* Automatic memory management.\n",
    "\n",
@@ -404,6 +396,13 @@
    "35 / 5"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Division is a bit weird: if you give it integer arguments, the result will also be an integer."
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 8,
@@ -424,13 +423,6 @@
    "36 / 5"
   ]
  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Division is a bit weird: if you give it integer arguments, the result will also be an integer."
-   ]
-  },
  {
   "cell_type": "markdown",
   "metadata": {
@@ -606,15 +598,12 @@
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
-     "slide_type": "subslide"
+     "slide_type": "slide"
    }
   },
   "source": [
-    "Python as a calculator\n",
-    "===\n",
-    "\n",
    "Variables\n",
-    "---\n",
+    "===\n",
    "\n",
    "* We can use names to reference values (variables).\n",
    "* No need to declare them first or define the type."
@@ -622,16 +611,17 @@
  },
  {
   "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
-    "a = 1.3e20"
+    "a = 1.3e20\n",
+    "b = 2"
   ]
  },
  {
   "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
@@ -640,7 +630,7 @@
       "1.3e+20"
      ]
     },
-     "execution_count": 16,
+     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
@@ -651,23 +641,23 @@
  },
  {
   "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
-       "2.84e+20"
+       "3.2e+20"
      ]
     },
-     "execution_count": 17,
+     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
-    "b = a + 1.2e19\n",
-    "b * 2"
+    "c = a + 1.5e19 * b\n",
+    "c * 2"
   ]
  },
  {
@@ -678,7 +668,7 @@
    }
   },
   "source": [
-    "Python's type system (1/2)\n",
+    "Python's type system (1/4)\n",
    "===\n",
    "\n",
    "Every value has a type, view it using `type`:"
@@ -746,8 +736,15 @@
  },
  {
   "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
   "source": [
+    "Python's type system (2/4)\n",
+    "===\n",
+    "\n",
    "Another example of a builtin datatype is `str`, we'll see more later:"
   ]
  },
@@ -775,13 +772,10 @@
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
-     "slide_type": "subslide"
+     "slide_type": "-"
    }
   },
   "source": [
-    "Python's type system (2/2)\n",
-    "===\n",
-    "\n",
    "Some operations are defined on more than one type, possibly with different meanings."
   ]
  },
@@ -807,14 +801,61 @@
  },
  {
   "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
   "source": [
+    "Python's type system (3/4)\n",
+    "===\n",
+    "\n",
    "Dynamic typing means that variables can be assigned values of different types during runtime."
   ]
  },
  {
   "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1.3e+20"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "float"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "type(a)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
@@ -823,7 +864,7 @@
       "str"
      ]
     },
-     "execution_count": 23,
+     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
@@ -835,8 +876,15 @@
  },
  {
   "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "slideshow": {
+     "slide_type": "subslide"
+    }
+   },
   "source": [
+    "Python's type system (4/4)\n",
+    "===\n",
+    "\n",
    "Python is strongly typed, meaning that operations on values with incompatible types are forbidden."
   ]
  },
@@ -860,6 +908,41 @@
    "'beer' + 34"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "<div class=\"alert alert-success\">\n",
+    "<h1>Hands on!</h1>\n",
+    "\n",
+    "<ol>\n",
+    "  <li>We’ve seen that b = 2 is legal.\n",
+    "    <ul>\n",
+    "      <li> What about 2 = b? </li>\n",
+    "      <li>How about a = b = 1?</li>\n",
+    "     </ul>\n",
+    "  </li>\n",
+    "  <li>In math notation you can multiply x and y like this: xy.\n",
+    "      What happens if you try that in Python?</li>\n",
+    "  <li>How many seconds are there in 42 minutes and 42 seconds?</li>\n",
+    "  <li>How many miles are there in 16 kilometers? Hint: there are 1.61 kilometers in a mile.</li>\n",
+    "  <li>Let's assume that you run a 42 kilometer race in 4 hours 42 minutes and 42 seconds.\n",
+    "    <ul>\n",
+    "      <li>What is your average pace (time per mile in minutes and seconds)?</li>\n",
+    "      <li>What is your average speed in miles per hour?</li>\n",
+    "    </ul>\n",
+    "  </li>\n",
+    "    <li>Use string operations to reference string 'tra la la la' in a variable named <i>song</i>.</li>\n",
+    "  <li>If an article costs 249 Euros including the 19% Value Added Tax (VAT), what is the actual VAT amount in Euros for the corresponding article?</li>\n",
+    "</ol>\n",
+    "\n",
+    "</div>"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 1,
@@ -898,7 +981,7 @@
       "</style>"
      ],
      "text/plain": [
-       "<IPython.core.display.HTML at 0x3463a50>"
+       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 1,
@@ -909,30 +992,54 @@
   "source": [
    "from IPython.display import HTML\n",
    "def css_styling():\n",
-    "    styles = open('styles/custom.css', 'r').read()\n",
+    "    styles = open('../styles/custom.css', 'r').read()\n",
    "    return HTML('<style>' + styles + '</style>')\n",
    "css_styling()"
   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "Acknowledgements\n",
+    "========\n",
+    "\n",
+    "Martijn Vermaat\n",
+    "\n",
+    "[Jeroen Laros](mailto:j.f.j.laros@lumc.nl)\n",
+    "\n",
+    "Based on\n",
+    "---------\n",
+    "[Python Scientific Lecture Notes](http://scipy-lectures.github.io/)\n",
+    "\n",
+    "License\n",
+    "--------\n",
+    "[Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
+   ]
  }
 ],
 "metadata": {
  "celltoolbar": "Slideshow",
  "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
   "language": "python",
-   "name": "python3"
+   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
-    "version": 3
+    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.12"
  }
 },
 "nbformat": 4,

 %% Cell type:markdown id: tags:

 <span style="font-size: 200%">Introduction to Python (1)</span>
 ===

-<br>
-
-[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)
-
-[Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)
-
-Based on: [Python Scientific Lecture Notes](http://scipy-lectures.github.io/)
-
-License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)
-
 %% Cell type:markdown id: tags:

 About Python
 ===

 History
 ---

 * Created early 90's by Guido van Rossem at CWI.
+  - Name: Monty Python.
 * General purpose, high-level programming language.
 * Design is driven by code readability.

 %% Cell type:markdown id: tags:

 About Python
 ===

 Features
 ---

 * Interpreted, no separate compilation step needed.
-* Imperative and object-oriented programming (and some functional programming).
+* Imperative and object-oriented programming.
+  - And some functional programming.
 * Dynamic type system.
 * Automatic memory management.

 We'll come back to most of this.

 %% Cell type:markdown id: tags:

 About Python
 ===

 Why Python?
 ---

 * Readable and low barrier to entry.
 * Rich scientific libraries.
 * Many other libraries available.
 * Widely used with a large community.

 %% Cell type:markdown id: tags:

 About Python
 ===

 Python 2 versus Python 3
 ---

 * Python 3 is backwards incompatible.
 * Some libraries don't support it yet.
 * Python 2.7 is the last Python 2.
 * Some Python 3 features are backported in Python 2.7.
 * Default Python on most distributions is Python 2.7.

 We use Python 2.7 for the time being.

 %% Cell type:markdown id: tags:

 Running Python code
 ===

 Two main ways of writing and executing Python code.

 Interactively
 ---

 * Statement by statement directly in the interpreter.

 Non-interactively
 ---

 * By editing in a file and running the code afterwards.

 %% Cell type:markdown id: tags:

 We'll start with the first option.

 %% Cell type:markdown id: tags:

 Running Python code
 ===

 The standard Python interpreter
 ---

 Start it by typing `python` on the command line:

    $ python
    Python 2.7.3 (default, Jan  2 2013, 13:56:14)
    [GCC 4.7.2] on linux2
    Type "help", "copyright", "credits" or "license" for more information.
    >>>

 * It shows an interpreter prompt.
 * You can give it Python code to interpret.

 %% Cell type:markdown id: tags:

 Running Python code
 ===

 The IPython interpreter
 ---

 * Similar to the standard Python interpreter, but with
 * syntax highlighting,
 * tab completion,
 * cross-session history, etcetera...

 Start it by typing `ipython` on the command line:

    $ ipython
    Python 2.7.3 (default, Jan  2 2013, 13:56:14)
    Type "copyright", "credits" or "license" for more information.

    IPython 0.13.1 -- An enhanced Interactive Python.
    ?         -> Introduction and overview of IPython's features.
    %quickref -> Quick reference.
    help      -> Python's own help system.
    object?   -> Details about 'object', use 'object??' for extra details.

    In [1]:

 %% Cell type:markdown id: tags:

 From now on, play along in your own IPython interpreter.

 %% Cell type:markdown id: tags:

 Python as a calculator
 ===

 Integers
 ---

 %% Cell type:code id: tags:

 ``` python
 17
 ```

 %% Output

    17

 %% Cell type:code id: tags:

 ``` python
 (17 + 4) * 2
 ```

 %% Output

    42

 %% Cell type:markdown id: tags:

 Python as a calculator
 ===

 Floating point numbers
 ---

 %% Cell type:code id: tags:

 ``` python
 3.2 * 18 - 2.1
 ```

 %% Output

    55.5

 %% Cell type:code id: tags:

 ``` python
 36. / 5
 ```

 %% Output

    7.2

 %% Cell type:markdown id: tags:

 Scientific notation:

 %% Cell type:code id: tags:

 ``` python
 1.3e20 + 2
 ```

 %% Output

    1.3e+20

 %% Cell type:code id: tags:

 ``` python
 1.3 * 10**20
 ```

 %% Output

    1.3e+20

 %% Cell type:markdown id: tags:

 Python as a calculator
 ===

 The division operator
 ---

 %% Cell type:code id: tags:

 ``` python
 35 / 5
 ```

 %% Output

    7

+%% Cell type:markdown id: tags:
+
+Division is a bit weird: if you give it integer arguments, the result will also be an integer.
+
 %% Cell type:code id: tags:

 ``` python
 36 / 5
 ```

 %% Output

    7

 %% Cell type:markdown id: tags:

-Division is a bit weird: if you give it integer arguments, the result will also be an integer.
-
-%% Cell type:markdown id: tags:
-
 Python as a calculator
 ===

 The division operator
 ---

 %% Cell type:code id: tags:

 ``` python
 35 / 5
 ```

 %% Output

    7

 %% Cell type:code id: tags:

 ``` python
 36 / 5
 ```

 %% Output

    7

 %% Cell type:markdown id: tags:

 Solution 1
 ---

 Give floating point arguments instead of integer arguments.

 %% Cell type:code id: tags:

 ``` python
 36. / 5.
 ```

 %% Output

    7.2

 %% Cell type:markdown id: tags:

 Python as a calculator
 ===

 The division operator
 ---

 %% Cell type:code id: tags:

 ``` python
 35 / 5
 ```

 %% Output

    7

 %% Cell type:code id: tags:

 ``` python
 36 / 5
 ```

 %% Output

    7

 %% Cell type:markdown id: tags:

 Solution 2
 ---

 From Python 3 onwards, division behaves differently. You can actually get that behaviour in Python 2.7:

 %% Cell type:code id: tags:

 ``` python
 from __future__ import division
 36 / 5
 ```

 %% Output

    7.2

 %% Cell type:markdown id: tags:

-Python as a calculator
-===
-
 Variables
---
+===

 * We can use names to reference values (variables).
 * No need to declare them first or define the type.

 %% Cell type:code id: tags:

 ``` python
 a = 1.3e20
+b = 2
 ```

 %% Cell type:code id: tags:

 ``` python
 a
 ```

 %% Output

    1.3e+20

 %% Cell type:code id: tags:

 ``` python
-b = a + 1.2e19
-b * 2
+c = a + 1.5e19 * b
+c * 2
 ```

 %% Output

-    2.84e+20
+    3.2e+20

 %% Cell type:markdown id: tags:

-Python's type system (1/2)
+Python's type system (1/4)
 ===

 Every value has a type, view it using `type`:

 %% Cell type:code id: tags:

 ``` python
 type(27)
 ```

 %% Output

    int

 %% Cell type:code id: tags:

 ``` python
 type(3.0 * 2.7)
 ```

 %% Output

    float

 %% Cell type:code id: tags:

 ``` python
 type(a)
 ```

 %% Output

    float

 %% Cell type:markdown id: tags:

+Python's type system (2/4)
+===
+
 Another example of a builtin datatype is `str`, we'll see more later:

 %% Cell type:code id: tags:

 ``` python
 type('I am a homo sapiens')
 ```

 %% Output

    str

 %% Cell type:markdown id: tags:

-Python's type system (2/2)
-===
-
 Some operations are defined on more than one type, possibly with different meanings.

 %% Cell type:code id: tags:

 ``` python
 'beer' * 5 + 'whiskey'
 ```

 %% Output

    'beerbeerbeerbeerbeerwhiskey'

 %% Cell type:markdown id: tags:

+Python's type system (3/4)
+===
+
 Dynamic typing means that variables can be assigned values of different types during runtime.

 %% Cell type:code id: tags:

 ``` python
+a
+```
+
+%% Output
+
+    1.3e+20
+
+%% Cell type:code id: tags:
+
+``` python
+type(a)
+```
+
+%% Output
+
+    float
+
+%% Cell type:code id: tags:
+
+``` python
 a = 'spezi'
 type(a)
 ```

 %% Output

    str

 %% Cell type:markdown id: tags:

+Python's type system (4/4)
+===
+
 Python is strongly typed, meaning that operations on values with incompatible types are forbidden.

 %% Cell type:code id: tags:

 ``` python
 'beer' + 34
 ```

 %% Output

    ---------------------------------------------------------------------------
    TypeError                                 Traceback (most recent call last)
    <ipython-input-24-ec918fbfdf41> in <module>()
    ----> 1 'beer' + 34

    TypeError: cannot concatenate 'str' and 'int' objects

+%% Cell type:markdown id: tags:
+
+<div class="alert alert-success">
+<h1>Hands on!</h1>
+
+<ol>
+  <li>We’ve seen that b = 2 is legal.
+    <ul>
+      <li> What about 2 = b? </li>
+      <li>How about a = b = 1?</li>
+     </ul>
+  </li>
+  <li>In math notation you can multiply x and y like this: xy.
+      What happens if you try that in Python?</li>
+  <li>How many seconds are there in 42 minutes and 42 seconds?</li>
+  <li>How many miles are there in 16 kilometers? Hint: there are 1.61 kilometers in a mile.</li>
+  <li>Let's assume that you run a 42 kilometer race in 4 hours 42 minutes and 42 seconds.
+    <ul>
+      <li>What is your average pace (time per mile in minutes and seconds)?</li>
+      <li>What is your average speed in miles per hour?</li>
+    </ul>
+  </li>
+    <li>Use string operations to reference string 'tra la la la' in a variable named <i>song</i>.</li>
+  <li>If an article costs 249 Euros including the 19% Value Added Tax (VAT), what is the actual VAT amount in Euros for the corresponding article?</li>
+</ol>
+
+</div>
+
 %% Cell type:code id: tags:

 ``` python
 from IPython.display import HTML
 def css_styling():
-    styles = open('styles/custom.css', 'r').read()
+    styles = open('../styles/custom.css', 'r').read()
    return HTML('<style>' + styles + '</style>')
 css_styling()
 ```

 %% Output

-    <IPython.core.display.HTML at 0x3463a50>
+    <IPython.core.display.HTML object>
+
+%% Cell type:markdown id: tags:
+
+Acknowledgements
+========
+
+Martijn Vermaat
+
+[Jeroen Laros](mailto:j.f.j.laros@lumc.nl)
+
+Based on
+---------
+[Python Scientific Lecture Notes](http://scipy-lectures.github.io/)
+
+License
+--------
+[Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)

--- a/introduction/02_introduction_to_python_2.ipynb
+++ b/introduction/02_introduction_to_python_2.ipynb
--- a/introduction/02_introduction_to_python_3.ipynb
+++ b/introduction/02_introduction_to_python_3.ipynb
--- a/more_python/03_more_python_goodness_1.ipynb
+++ b/more_python/03_more_python_goodness_1.ipynb
--- a/more_python/03_more_python_goodness_2.ipynb
+++ b/more_python/03_more_python_goodness_2.ipynb
--- a/visualization/data/populations.csv
+++ b/visualization/data/populations.csv
+,Year,Belgium,Denmark,Netherlands,Sweden
+0,1950,17.278599999999997,8.5627,20.2273,14.0332
+1,1951,17.3564,8.607399999999998,20.528799999999997,14.140799999999999
+2,1952,17.4608,8.6676,20.7642,14.248899999999999
+3,1953,17.555500000000002,8.7386,20.986,14.3429
+4,1954,17.6388,8.811399999999999,21.2307,14.4272
+5,1955,17.7367,8.8784,21.5018,14.5247
+6,1956,17.8477,8.9328,21.7792,14.6314
+7,1957,17.9787,8.9757,22.0527,14.734300000000001
+8,1958,18.1051,9.0302,22.373600000000003,14.8306
+9,1959,18.2072,9.0932,22.6954,14.907499999999999
+10,1960,18.2376,9.1621,22.973399999999998,14.9607
+11,1961,18.331699999999998,9.2338,23.2775,15.0413
+12,1962,18.436799999999998,9.2939,23.6113,15.1232
+13,1963,18.566200000000002,9.3672,23.931600000000003,15.2087
+14,1964,18.7339,9.4404,24.2543,15.3228
+15,1965,18.896,9.516200000000001,24.5893,15.4678
+16,1966,19.015700000000002,9.595,24.9128,15.6157
+17,1967,19.1129,9.6775,25.1965,15.7355
+18,1968,19.179699999999997,9.729700000000001,25.4594,15.8246
+19,1969,19.2252,9.781500000000001,25.7561,15.936
+20,1970,19.275399999999998,9.8576,26.076999999999998,16.085700000000003
+21,1971,19.346600000000002,9.901399999999999,26.3891,16.1967
+22,1972,19.4222,9.9512,26.6567,16.2449
+23,1973,19.4836,10.0152,26.8784,16.2738
+24,1974,19.5131,10.0905,27.0903,16.320700000000002
+25,1975,19.6017,10.108799999999999,27.3328,16.3854
+26,1976,19.6363,10.1451,27.548000000000002,16.4448
+27,1977,19.660600000000002,10.1766,27.7125,16.502899999999997
+28,1978,19.674599999999998,10.2087,27.8837,16.5517
+29,1979,19.6968,10.2336,28.0765,16.587400000000002
+30,1980,19.7103,10.245999999999999,28.2994,16.6209
+31,1981,19.6976,10.243400000000001,28.4942,16.641
+32,1982,19.714599999999997,10.2355,28.625500000000002,16.6503
+33,1983,19.716,10.2286,28.7339,16.658
+34,1984,19.706,10.2232,28.848399999999998,16.6732
+35,1985,19.7165,10.2274,28.9833,16.7008
+36,1986,19.729599999999998,10.2408,29.144199999999998,16.7396
+37,1987,19.7404,10.254,29.3305,16.795699999999997
+38,1988,19.8034,10.2586,29.5202,16.873
+39,1989,19.8754,10.2646,29.698,16.9859
+40,1990,19.934800000000003,10.2798,29.903,17.1173
+41,1991,20.0092,10.3081,30.1391,17.2273
+42,1992,20.0903,10.3404,30.3681,17.3364
+43,1993,20.1674,10.378499999999999,30.5811,17.4373
+44,1994,20.230800000000002,10.4101,30.7657,17.5621
+45,1995,20.2735,10.4558,30.9179,17.654
+46,1996,20.313285999999998,10.523299999999999,31.061,17.6821
+47,1997,20.340452,10.5686,31.2216,17.6925
+48,1998,20.406016,10.602599999999999,31.4146,17.702399999999997
+49,1999,20.452844,10.63822,31.624,17.716102
+50,2000,20.502511,10.674688,31.851039,17.744588
+51,2001,20.573149,10.710163999999999,32.092372999999995,17.792254
+52,2002,20.665584000000003,10.74851,32.297866,17.849916
+53,2003,20.752265,10.774348,32.450617,17.916458
+54,2004,20.842273,10.802354000000001,32.563558,17.987062
+55,2005,20.957247000000002,10.831956,32.64002,18.059144
+56,2006,21.0959255,10.869133999999999,32.692484,18.161009
+57,2007,21.251411,10.91483,32.763406,18.296198
+58,2008,21.419958,10.978044,32.891203000000004,18.439287
+59,2009,21.592997,11.038882000000001,33.060784999999996,18.597040999999997
+60,2010,21.67981,11.087638,33.230799000000005,18.756252
+61,2011,22.001275999999997,11.133712,33.386160000000004,18.898439
+62,2012,22.189700000000002,11.17417,33.509935999999996,19.038762
+63,2013,22.356872,11.217568,33.608877,19.200757
+64,2014,22.454566,11.279437999999999,33.608877,19.392219
+65,2015,,,33.879855,19.392219