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Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2019/20



10 Feb 2019: Schedule online.
16 Jan 2019: Workshop is fully booked.


5-day course 17.-21.02.2020 9:00-15:00 (room open until 16:00) Takustr. 9, r.006 (ground floor)


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 Python and Jupyter notebooks. We will provide test data, but participants may also bring their own MD data (any standard format, e.g., xtc, dcd) and we will help with applying PyEMMA to them.

Please bring your own laptop. Participants without Eduroam access will get a temporary login for the campus wifi.



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).

Preliminary schedule

Mon Tue Wed Thu Fr
09-12 lectures/tutorials lectures/tutorials lectures tutorials contributed talks projects
12-13 lunch break lunch break lunch break lunch break lunch break
13-15 lectures/tutorials lectures/tutorials lectures/tutorials projects* student talks

*On Thursday afternoon, assistants will be available until 17h to assist with projects.



Welcome (5 min, Tim Hempel)
PyEMMA package development / intro to installation session (10 min, Moritz Hoffmann)
Installation (45 min)
Introduction (45 min, Frank Noé)
[Break 15 min]
data I/O, featurization, dimension reduction, clustering incl. tutorial (60 min, Tim Hempel)
[lunch break ~1h]
MSM theory (50 min, Simon Olsson)
MSM estimation + validation tutorial (60 min, Fabian Paul)


Brief repetition (10 min, Tim Hempel)
VAMP theory (20-30 min, NN)
I/O, Vamp, MSM estimation mini project (30+ min)
MSM analysis + CG + TPT incl. tutorial (120 min, Fabian Paul)
[lunch break ~1h]
MSM analysis mini project (30 min)
HMM theory and tutorial (60 min, Simon Olsson)


Brief repetition (10 min, Tim Hempel)
Enhanced sampling + MEMMs (60 min, Fabian Paul)
MEMM mini project(s) (90 min)
[lunch break ~1h]
VAMPNets intro (30 min, Luca Pasquali)
VAMPNets mini projects (60 min)
Lectures wrap-up (10 min, Tim Hempel)

Preparation for course

Installation of PyEmma

For tutorials, we will use the Python-based software package PyEMMA (Emma's Markov Model Algorithms,, We strongly recommend to install PyEMMA from the anaconda Python distribution via conda install -c conda-forge pyemma
If you are not using the anaconda Python distribution, PyEMMA is also available via source installation from Github. For more detailed installation instructions, please refer to
If possible, install the latest release of PyEMMA.

Wifi Access

Please check your wifi access after arrival at the institute. If your home institute supports eduroam, log in to the "eduroam" network with your username and home domain (i.e.,
For participants without eduroam access, FU provides the wifi network "conference". A log-in code will be posted on the first day. Please find the official Documentation here.

Materials and Videos

To give you an idea of the workshop content and focus see here
Link to youtube playlist from 2017
Link to youtube playlist from 2018
Link to workshop material on Github

Information for students


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


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.

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 to their simulations. To inquire about free spots, send an email to tim.hempel[at] stating your affiliation and research focus. There is no official registration required. We will put you on the course roster and mailing list. On the first day of the workshop you will sign the participants' list at the registration desk and receive a certificate after the workshop.

Information for participants from outside of Berlin

How to find us

The workshop takes place at Freie Universität, Institute of Computer Science, Takustr. 9, 14195 Berlin
Important: Although the official address is Takustr. 9, 14195 Berlin, the building itself is inset from the road and best accessed via a footpath from Arnimallee 6 (past the building with signature number Pi strip running along the walls).

The seminar is in the grey brick building on the ground floor, r. 006. There will be sign posts.

Nearest metro stop is U Dahlem-Dorf on the U3 line (walking distance 7 min. as seen on map)
Nearest bus stop is "Arnimallee" on the Bus X83 route (connecting U Dahlem with S+U Rathaus Steglitz).
The way to the workshop will be signposted from the top of Arnimallee.

Alternative access from the southside is via the Altensteinstraße 23 car park. Nearest busstop here is “Limonenstr." on the Bus 101 route. From car park follow the driveway until you arrive here.

For official directions to institute and area map see here.
For googlemaps search use "Institute of Computer Science, 14195 Berlin"


Freie Universität does not operate on-campus guest houses or student dormitories. Therefore, participants from outside of Berlin must arrange their own accommodation. A good budget choice near campus is Residenz 2000 Aparthotel. For more links see the university's accommodation listing.
For a quick search of available accommodation use Set destination to "14195, Berlin" and "lowest price first". This should bring up numerous value deals within traveling distance from campus. The option “open in this map” is very useful in determining the distance from campus. Districts well connected to campus are Steglitz-Zehlendorf, Tempelhof-Schöneberg, Charlottenburg-Wilmersdorf as well as anything within the so called 'Ringbahn' loop. You can also check travel times from accommodation to FU on pubic transport journey planner

Getting around

Berlin has an extensive public transit network (undergound, urban rail, buses, trams) with 3 tariff zones. Ticket AB (2.80€) will get you anywhere in Berlin including Tegel Airport (TXL). For Schönefeld Airport (SFX) you will need Ticket ABC (3.40€). For more information see Tripadvisor Guide to Berlin Public Transport.


The workshop takes place during term break and the nearby student cafeteria will be closed. We will provide beverages, biscuits & sweets for coffee breaks. For lunch please bring your own provisions or use one of the following options:

FU Mensa | canteen | Otto-von-Simson-Str. 26 | menu | mensa card
Kantine Julius-Kühn-Institut | canteen |
Baci's Coffee | coffee shop | Königin-Luise-Str. 39 | soups, bagel, cakes
Asia Snack Dahlem | vietnamese | Königin-Luise-Str. 38
eßkultur in den Museen Dahlem | international | Takustr. 38-40 (via car park)


Name Mail
Tim Hempel coordinator tim.hempel[at]
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