Context-based generation of kinetic equations with SBMLsqueezer 1.3

Abstract

The development of predictive, quantitative models constitutes a common task in today‘s systems biology. To obtain a mathematical model description for the simulation of gene-regulatory, signaling, and metabolic networks, kinetic equations are required for each reaction within the network. Deriving and assembling these formulas is a complicated, time-consuming, and error-prone process that requires knowledge about the structure of interactions, consistently choosing a rate law for each type of reaction, and assignment of appropriate units to all parameters. In many cases, thermodynamic dependencies between the parameters have to be taken into account. For multi compartment models, the concentration units of reacting species have to be converted into molecular amounts. Here we present version 1.3 of the program SBMLsqueezer that generates kinetic equations for SBML models based on the definition of the network's topology and annotations of the elements therein, i.e., Systems Biology Ontology (SBO) and Minimal Information Requested In the Annotation of Models (MIRIAM) annotations.