Presentations

Talk at the Jamboree 2021 about epigenomic map of human liver zonation and loss of zonation in end-stage liver disease

Jamboree presentation

Computational modeling and simulation become increasingly important for Systems Medicine. A number of corresponding software tools have been developed but require scientists to encode their models in an imperative programming language. Morpheus [1,2], on the other hand, is an extensible open-source software framework that is entirely based on declarative modeling. It uses the domain-specific language MorpheusML to define multicellular models through a user-friendly GUI and has since proven ...

PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Computational Modeling Jan Grzegorzewski, Janosch Brandhorst, Dimitra Eleftheriadou, Kathleen Green, Matthias König bioRxiv 760884; doi: https://doi.org/10.1101/760884

Workshop from LiSyM retreat in January 2020. Additional slides devoted to Social Media for Academics. Developed by Peter Krinenberg from https://naturalscience.careers/

We face a reproducibility crisis and computational science, with most published models neither being accessible nor reproducible. The Systems Biology Markup Language (SBML) is the de facto standard format for encoding pathway based models, which provides a means for exchanging process based models between researchers and tools. The talk gives an overview of SBML and SBML-based tools.