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+{
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+ "metadata": {
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+ "source": [
+ "<span style=\"font-size: 200%\">Programming in Python</span>\n",
+ "===\n",
+ "\n",
+ "<br>\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "About the course\n",
+ "===\n",
+ "\n",
+ "* Aimed at PhD students, Postdocs, researchers, analysts, ...\n",
+ "* Programming as a tool to do your research.\n",
+ "* Slightly focussed on bioinformatics.\n",
+ "\n",
+ "**Note:** This is its third session."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Teachers\n",
+ "===\n",
+ "\n",
+ "* Jeroen Laros<br>\n",
+ " [j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Mihai Lefter<br>\n",
+ " [m.lefter@lumc.nl](mailto:m.lefter@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Jonathan Vis<br>\n",
+ " [j.k.vis@lumc.nl](mailto:j.k.vis@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Mark Santcroos<br>\n",
+ " [m.a.santcroos@lumc.nl](mailto:m.a.santcroos@lumc.nl)\n",
+ "\n",
+ "\n",
+ "* Guy Allard<br>\n",
+ " [w.g.Allard@lumc.nl](mailto:w.g.allard@lumc.nl)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "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",
+ "\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)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Software requirements\n",
+ "===\n",
+ "\n",
+ "* Anaconda\n",
+ " * Python 2.7\n",
+ " * NumPy, matplotlib, Biopython\n",
+ "* Git\n",
+ "\n",
+ "Anaconda installation instructions [here](https://docs.anaconda.com/anaconda/install/)."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Exercises\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."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "slideshow": {
+ "slide_type": "slide"
+ }
+ },
+ "source": [
+ "Getting help\n",
+ "===\n",
+ "\n",
+ "* Ask a teacher.\n",
+ "* If it's private, mail one of the teachers.\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
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+ "slide_type": "skip"
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+ "\n",
+ "/* Workaround some highlight.js bugs in language autodetection. */\n",
+ "code.objectivec *,\n",
+ "code.perl *,\n",
+ "code.cs *,\n",
+ "code.javascript *,\n",
+ "code.http * {\n",
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+ "source": [
+ "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)\n"
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