diff --git a/INSTALL.md b/INSTALL.md index e93e6a0fff2cebc02f76bcf26dbca0b855e6e513..e984346d5d9a7fd0d9ea71ed7f4dfa37117ba3cd 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -8,7 +8,7 @@ packages installed. Linux ----- -We assume Ubuntu (12.10 Precise Pangolin or later) or Debian Linux (7.0 Wheezy +We assume Ubuntu (12.04 Precise Pangolin or later) or Debian Linux (7.0 Wheezy or later), but if you manage to install everything on a different flavour that's also fine. diff --git a/README.md b/README.md index c29e86aab149954620fb5a62e47fa81f6eb90202..1fe0d8a63b9699625436409340bc5b41bab44464 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ Programming course ================== -This repository contains material for the first installment (August 2013) of -a programming course for scientists organised by the department of Human +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 @@ -23,35 +23,52 @@ Software installation See the instructions in `INSTALL.md`. -Slides ------- +Materials +--------- -The top-level directory contains slides for the following lessons. +The top-level directory contains materials for the following lessons: -1. [Welcome](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/welcome.ipynb) -2. [Introduction to Python](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/python.ipynb) -3. [Version control with Git](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/git.ipynb) -4. [More Python Goodness](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/more-python.ipynb) -5. [Working with NumPy arrays](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/numpy.ipynb) -6. [Plotting with matplotlib](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/matplotlib.ipynb) -7. [Object-oriented programming](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/classes.ipynb) -8. [A sip of Biopython](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/biopython.ipynb) +1. Welcome (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/welcome.ipynb) +2. Introduction to Python (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/python.ipynb) +3. More Python Goodness (notebook) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/more-python.ipynb) +4. Working with NumPy arrays (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/numpy.ipynb) +5. Plotting with matplotlib (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/matplotlib.ipynb) +6. Object-oriented programming (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/classes.ipynb) +7. A sip of Biopython (notebook) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/biopython.ipynb) -Note: These links are to one-page renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/), see below how to get the real slideshows. +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/). -Editing the slides ------------------- +Notebooks +--------- -The slides are simple IPython notebooks, you can edit them by starting a -notebook server: +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). +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