The tool Snoopy provides a unifying Petri net framework which has particularly many
application scenarios in systems and synthetic biology. The framework consists of two …

To investigate biomolecular networks, Snoopy provides a unifying Petri net framework
comprising a family of related Petri net classes. Models can be hierarchically structured …

A review of mathematical modeling in metal metabolism is presented. Both endogenous and
exogenous metals are considered. Four classes of methods are considered: Petri nets, multi …

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA
is a high-level language for modelling biological systems such as metabolic pathways and …

In the study of complex patterns in biology, mathematical and computational models are
emerging as important tools. In addition to experimental approaches, these modeling tools …

Petri nets have become an effective formalism to model biological systems. However,
attempts to simulate biological systems by low-level Petri nets are restricted to relatively …

For the implementation of the virtual cell, the fundamental question is how to model and
simulate complex biological networks. During the last 15 years, Petri nets have attracted …

Background Cancer stem cell theory suggests that cancers are derived by a population of
cells named Cancer Stem Cells (CSCs) that are involved in the growth and in the …

The detection and analysis of structural invariants in cellular reaction networks is of central
importance to achieve a more comprehensive understanding of metabolism. In this work, we …

We present a case study of reusing parameters and reactions of a deterministic model of a
biochemical system in order to implement a stochastic one. Our investigations base on a …