Python programming course

On this Wiki you'll find information such as a program and course material for the programming course 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. There will be a focus on bioinformatics and programming to suppor scientific research in general.

The program consists of four mornings with lessons and some assignments to be done in your own time (i.e., during the afternoons).

The next installment will be in the week of July 14-18, 2014. Registration is required and handled by MGC. Register at their website.

The organizers



Day Time Lesson Keywords Teacher
Monday 09-10 Welcome, Introduction to Python (1) arithmetic, variables, types Martijn
10-11 Introduction to Python (2) container types, control flow, iteration Jeroen
11-12 Introduction to Python (3) functions, objects, files Michiel
Tuesday 09-10 More Python goodness (1) strings, comments, errors Michiel
10-11 More Python goodness (2) modules, standard library, input/output Wai Yi
11-12 Working with NumPy arrays indexing, slicing, reductions, broadcasting Martijn
Wednesday 09-10 IPython Notebook reproducible research, cell types Michiel
10-11 Plotting with matplotlib plotting, figure layout Jeroen
11-12 Painting Pandas data frames, reading data, plot types Wai Yi
Friday 09-10 Object-oriented programming classes, special methods, inheritance Jeroen
10-11 A sip of Biopython (1) packages, sequences Wai Yi
11-12 A sip of Biopython (2) input/output, online resources, blast Martijn

Instruction for uploading assignment solutions for review

Our etherpad is at

Location: room J1-83, LUMC building 1.


The following are required before taking the course:

We recommend taking our course on version control with git first, but this is not required.

We can provide you with a laptop that has all the required software installed. You can also use your own laptop, but make sure it has the necessary software installed (see below). The lessons are interactive, meaning that you really need a laptop.

Software installation

See Software installation.


You can contact Martijn Vermaat or any of the other teachers for more information.

Last modified 4 years ago Last modified on Feb 23, 2015 12:58:25 PM

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