denbi-modsim

Tools for systems biology modeling and data exchange

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. The first day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The second day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI.

NEWS

We all have been following the COVID-19 pandemic these past weeks and months. For the longest time we hoped, that we would have been able to hold the workshop on “Tools for systems biology modeling and data exchange”, in Magdeburg on 27th-29th April 2020.

However, it has become apparent, that it won’t be possible to carry out the workshop. And so, we unfortunately must cancel the workshop at this time.

Due to the focus on hands on exercises, we don’t feel that an online presentation would be adequate.

However, the organizers plan on holding the workshop later this year, we will inform you as soon as we have fixed a new date.

Educators:

Educators: Steffen Klamt, Axel von Kamp, Sven Thiele, Ursula Kummer, Frank T. Bergmann (de.NBI-SysBio), Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS)

Date:

CANCELLED (was 27th April 10:00 am – 29th April 2020, 4:00pm)

Location:

MPI Magdeburg, Sandtorstrasse 1, 39106 Magdeburg, Germany

Accomodation

While there is no registration fee, attendees are expected to arrange for their travel and accommodation. The following hotels are recommended:

More information

Parameter Estimation

For the parameter estimation part, we have this archive, containing some models and data files to use during the tutorial. Second dataset for model selection of basic model.

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