Moved into a special folder the 2014 course session materials.

past_sessions/2014_july/README.md

+Programming course
+==================
+
+This repository contains material for the second installment (July 2014) of a
+programming course for scientists organised by the department of Human
+Genetics of the Leiden University Medical Center.
+
+The course is targeted at PhD students, Postdocs, or anyone willing to learn
+how to program in Python. Students are assumed to have some experience with
+programming, but not necessarily in Python, and the UNIX shell.
+
+The program consists of four mornings with lessons and some assignments to
+be done in your own time (i.e., during the afternoons).
+
+See the
+[Trac Wiki](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse)
+for more information.
+
+Software installation
+---------------------
+
+See the instructions in `INSTALL.md`.
+
+
+Materials
+---------
+
+The top-level directory contains materials for the following lessons:
+
+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/past_sessions/2014_july/01%20-%20Welcome.ipynb
+[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(1).ipynb
+[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(2).ipynb
+[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(3).ipynb
+[lesson_03_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(1).ipynb
+[lesson_03_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(2).ipynb
+[lesson_04]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/04%20-%20Working%20with%20NumPy%20arrays.ipynb
+[lesson_05]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/05%20-%20IPython%20Notebook.ipynb
+[lesson_06]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/06%20-%20Plotting%20with%20matplotlib.ipynb
+[lesson_07]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/07%20-%20Painting%20Pandas.ipynb
+[lesson_08]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/08%20-%20Object-oriented%20programming.ipynb
+[lesson_09_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(1).ipynb
+[lesson_09_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/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/humgen/programming-course-assignments).
+
+
+Notebooks
+---------
+
+We apply some custom styling to the notebooks (e.g., body width, font), which
+is loaded in the last cell. This loads `styles/notebook.css` and
+`styles/notebook.js`.
+
+A variant `styles/notebook.css.small` is provided that is more suitable for
+use on low-resolution displays. To use it, manually change the reference to
+this file in the bottom cell, and rerun it.
+
+
+Slideshows
+----------
+
+The sources for the slideshows are also IPython notebooks and you can edit
+them by starting a notebook server:
+
+    ipython notebook
+
+Choose *Slideshow* in the *Cell Toolbar* menu.
+
+Some aditional information on editing slides in the Notebook can be found
+here in
+[this presentation](http://www.slideviper.oquanta.info/tutorial/slideshow_tutorial_slides.html).
+
+We also apply some custom styling to the slideshows, which is loaded in the
+last cell.
+
+
+Live rendering of the slides
+----------------------------
+
+You can use nbconvert to convert the slides to HTML and serve them. For
+example:
+
+    ipython nbconvert --to slides --post serve numpy.ipynb
+
+This will open the slides in a new browser window. If you don't want that, add
+this argument:
+
+    --ServePostProcessor.open_in_browser=False
+
+To serve on another IP address than the default 127.0.0.1, use the `ip`
+configuration of the serve postprocessing. For example, to listen on all IP
+addresses:
+
+    --ServePostProcessor.ip=0.0.0.0
+
+Changing the port can be done similarly with `port`.
+
+By default, the reveal.js library is loaded over the internet from a CDN. I
+think it's usually not a good idea to rely on internet connectivity for your
+slides, so you can also place a copy of reveal.js on your local computer and
+specify the location like this:
+
+    --reveal-prefix reveal.js
+
+This would look for the reveal.js library in the `reveal.js` directory. A Git
+submodule is already setup for this, so you can just do:
+
+    git submodule init
+    git submodule update
+
+(Unfortunately, there are other online dependencies such Font Awesome, so
+without an internet connection, not everything will look ok, but it will
+work.)
+
+Also, if you just want to compile the slides to HTML without serving them to
+your browser, leave out the `--post serve` argument.