In this 1-week compact course (Blockseminar) participants will learn to construct Markov models for molecular dynamics simulation data and how to analyze them quantitatively. The course will take place in a computer lab and will include both theory lessons (20-30%) as well as practical applications using the software package PyEMMA (Emma's Markov Model Algorithms). All computer applications will be done in IPython. We will provide test data, but participants may also bring their own MD data (any standard format, i.e.xtc, dcd) and we will help with applying EMMA to them.