COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology

This tutorial workshop is a satellite of the 20th International Conference on Systems Biology (ICSB). Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats and how they support reproducible and FAIR computational modelling.

The topics covered will include: • Reproducibility and FAIR (Findable, Accessible, Interoperable and Re-usable) data • Curation services • Model setup using different software tools and systems biology platforms • Using experimental data for setting up quantitative models • Parameter estimation, optimization and model fitting • Simulation, analysis and visualization of biochemical models, and multicellular modelling • Constraint-based and logical modeling of metabolic and signaling networks • Database supported modelling: integrated data management and model databases • Community standards and formats for systems and synthetic biology models • Machine learning for model reduction and image analysis