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Welcome to the Computer Tutorial in Markov Modeling WS 2021/22

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The workshop is booked out!

This year's workshop will for the second time feature PyEMMA and DeepTime.


5-day course 21.-25.02.2022 12:00 noon online
IMPORTANT: On Monday, we will start one hour later at 1 pm.


In this 1-week compact course (Blockseminar) participants will learn how to quantitatively analyze time-series data, with a special focus on molecular dynamics simulations. Due to the COVID-19 pandemic, the course will take place online and will include both theory lessons (20-30%) as well as practical applications using the software packages PyEMMA and DeepTime. All computer applications will be done in Python and Jupyter notebooks. We will provide test data, but participants may also bring their own data (any standard format, e.g., xtc, dcd) and we will help with applying PyEMMA or DeepTime to it.



Theory lessons and associated software application sessions take place Monday to Wednesday. Thursday morning is dedicated to contributed talks. There is an open space for project work from Thursday afternoon to Friday noon. During this time, we will be available to support external scientists with their own projects and FU students with project tasks (to be presented on Friday afternoon).


The time is in local Berlin time (GMT+1).

Monday (13:00) Tuesday (12:00) Wednesday (12:00) Thursday (12:00) Friday (12:00)
Welcome, Tim Hempel, 15min Discuss homework, 30 min Discuss homework, 30 min Coherent sets and other Koopman methods (kCCA, KVAD), Moritz Hoffmann, 1-2h Student projects
Installation session + package development, Moritz Hoffmann, 45min MSM analysis (TPT, PCCA etc), Lluis Raich, 2h TRAM, Maaike Galama, 1h Independent Markov decomposition, Tim Hempel, 45min  
MSM theory, Tim Hempel, 1h   HMM + Tutorial, Simon Olsson, 1h contributed talks  
data / io / featurization, Moritz Hoffmann, 1h        
Break 1h Break 1h Break 1h Break 1h  
VAMP & VAC, Moritz Hoffmann, 30 min MSM debugging, Tim Hempel, 30min VAMPNet theory, Andreas Mardt, 30min Student projects Student presentations
MSM estimation tutorial, Lluis Raich, 1h TRAM, Maaike Galama, 1.h VAMPNet tutorial, Andreas Mardt, 1.5h Student projects Student presentations

*Assistants will be available on Friday morning from 9:30 a.m. to help with projects.



Preparation for course

Installation of PyEmma

For tutorials, we will use the Python-based software packages PyEMMA (Emma's Markov Model Algorithms,, and DeepTime (, We strongly recommend to install both packages from the anaconda Python distribution using the installation instructions provided here:
If you are not using the anaconda Python distribution, PyEMMA and DeepTime are also available via source installation from Github.
If possible, install the latest release of PyEMMA and DeepTime.

Information for students


Course ID: 20112011 Language: English
SWS:2; LP/Credits: 5

Registration for students of FU Berlin

FU students who were unable to register in Campus Management but registered with us should do a manual "Modulanmeldung" after the course. You find the form on the Registrar's office website. Complete and drop into mail box outside of registrar's office. Once you've been added to the course roster we can confirm your successful participation.

Registration for external participants

Please sign up here:

Credit Requirements (Scheinkriterien)

  • Active participation: Students will get project assignments (usually teams of two) on Wednesday, will work on their project on Thursday afternoon and Friday morning, and present on Friday afternoon (15 mins per team, both students should present).
  • For physics students, this course counts as a seminar "Selected Topics in Physics" (5 LP)
  • All participants will receive a certificate of attendance after the workshop by email.
  • FU students will get their credits assigned in Campus Management
  • Students from other unis can pick up a paper certificate (Schein) stating their credits on the last day of the workshop.

Information for non-resident applicants

As every year, we can offer a limited number of placements for PhD students and PostDocs interested in applying PyEmma or DeepTime to their simulations. To inquire about free spots, send an email to moritz.hoffmann[at] stating your affiliation and research focus. There is no official registration required. We will put you on the course roster and mailing list.

Information for participating

We will post the links to participate here.


Name   Mail
Moritz Hoffmann coordinator moritz.hoffmann[at]
Tim Hempel coordinator tim.hempel[at]

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