deNBI-Workshop: 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 first day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third 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 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.

Given the current situation, the workshop will be held as a virtual meeting (online course). We will send around a zoom link in the week prior to the workshop.

Prerequisites:

Some knowledge of mathematical modeling will be advantageous. The participants should have MATLAB and Python (including the “requests” package) installed. If you do not have MATLAB please let us know during registration, so we can send you information on how to obtain a trial license.

Educators:

Steffen Klamt
Axel von Kamp
Sven Thiele (MPI Magdeburg)
Ursula Kummer
Frank T. Bergmann (Heidelberg University)
Maja Rey
Andreas Weidemann
Ulrike Wittig (HITS)