Stefan Hoops

TL;DR: COPASI is presented, a platform-independent and user-friendly biochemical simulator that offers several unique features, and numerical issues with these features are discussed; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in Stochastic simulation.

TL;DR: Three ontologies created specifically to address the needs of the systems biology community are described, including the Systems Biology Ontology, which provides semantic information about the model components, and the Kinetic Simulation Algorithm Ontology and the Terminology for the Description of Dynamics, which categorizes dynamical features of the simulation results and general systems behavior.

TL;DR: Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis, global optimization, parameter estimation, and stochastic simulation.

TL;DR: This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core, which defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language.

TL;DR: The latest edition of the Systems Biology Markup Language (SBML) is reviewed, a format designed for this purpose that leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models.