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README.md

Programming course

This repository contains material for the first installment (August 2013) 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 for more information.

Software installation

See the instructions in INSTALL.md.

Slides

The top-level directory contains slides for the following lessons.

  1. Welcome
  2. Introduction to Python
  3. Version control with Git
  4. More Python Goodness
  5. Working with NumPy arrays
  6. Plotting with matplotlib
  7. Object-oriented programming
  8. A sip of Biopython

Note: These links are to one-page renderings on IPython Notebook Viewer, see below how to get the real slideshows.

Editing the slides

The slides are simple IPython notebooks, 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.

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

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:

--RevealHelpTransformer.url_prefix=reveal.js

This would look for the reveal.js library in the reveal.js directory. You can download reveal.js by cloning its GitHub repository:

git clone https://github.com/hakimel/reveal.js.git

Also, if you just want to compile the slides to HTML without serving them to your browser, leave out the --post serve argument.